Biologist - Planet Population +30% - needs some big boosts to make it even with the big boys
Level 200 - Taming the Vap - While a biologist all your planets are immune to Bio Vaporizers ~ Like this, but I'd personally go with reducing it by 75% effectiveness. But that's just me -- not big on full immunity.
Level 600 - Bio Warfare - Base Attack +20% - On NPC/PVP Your attacks have a 5% chance to to inflict Chemical Explosion giving target -2% att/def stackable to 20% max. Effects last 2 minutes and are immune to Caging ~ sounds fun, and I like it. What happens if 10 Biologists attack a boss? Is the 20% max per individual or is it 20% total?

Physicist - Max Shielding +30% - needs some big boosts to make it even with the big boys
Level 200 - Breakthrough in Krionite Defense - Ship is immune Krionite torpedoes and chaostatic Inhibitors ~ See previous comment regarding full immunity.
Level 600 - Look Mom I'm going to college! - 40 hour cool down - Planet Structure University Research Lab - Size 1 Arti 2 Research 2 - Increases owners chance for planetary event (think scientific breakthrough blahblah) by .05% ~ I like this, but with shields being what they are, the profession still seems a weaker than others. A small bonus to planetary shields at rank 600 -- even just 10% -- might make a difference.

Spy - Cloaking +20% - needs some big boosts to make it even
Level 200 - Spy Training #1 - 30 minute cool down When activated on player provides same info as spy probe Weap/Def/Resources when activated on a planet provides same info as spy probe governance and tracer ~ Since we already have tracers, and they aren't that hard to get, I'd suggest swapping this out for a "spymaster" passive ability granted at 600 that gives a small passive bonus to scan, attack, and critical percent (perhaps 5/5/10% would be sufficient?)
Level 600 - Spy Training #2 - 24 hour cool down allows you to spy on legion allowing you to see which users are online (same view you see in legion of members online) ~ like this a lot, but I would make it the level 200 ability

Raider - Raiding Strength +30% - again less used class needs some good boosts
Level 200 - Who you calling a scoundrel? Passive - Successful Raids return 50% more resources. and Scavenge - 48 hour cool down - Allows a second raid chance on base ~ this is awesome. That is all.
Level 600 - Illegal Planet Poaching - 24 hour cool down establish a blockade on enemy planet. While blockade is active you gain 50% of planetary production. Blockades will show up as an analyze ability on a planet but no notification is given to affected enemy. If planet owner does notice and clicks the analyze the blockade will become active in bt and will be able to be disabled at which point Raider will be able to be linked to. Poachers return home after 5 days if undetected. ~ again. Awesome.

Fixer - one of the most common classes in the game.. should get something but nothing crazy powerful
Level 200 - Tinker - Able to get a little more raw material off scrappin stuff +50% to all items scrapped
Level 600 - Workshop - 40 hour cooldown able to build a fixer workshop on a planet size 1 all resources 1 research +3% ~ both suggestions are nice, and not OP for an already popular/powerful profession. For some reason, mining seems more appropriate, but that's just me.

Explorer - Scan +20% - Good class but need to get them something that would make you want to stay one when you aren't scanning for planets
Level 200 - Explorer at Heart - Upon colonization / invade significantly increased chance of positive planetary event at +100% effectiveness ~ woo hoo!
Level 600 - Belly of the Beast - Adept at ferreting out those elusive big bosses - 24 hour cool down Find one random npc from the Rare/Extremely Rare class ~ also a good idea. Might make me stay an Explorer for more than a few hours at a time.

Excavator - Arti +10% - Easily most used class in the game should only get minor abilities
Level 200 - Guarding your investment - passive - while guarding a planet you own that planet gets the following bonuses Att+5% Def +5% Cloak +100%
Level 600 - The Big Dig! - 24 hour cool down - Attempt an excavation on a planet you own. a Planet can only have one attempt every 90 days.. Prizes should be something like 50% Nada, 25% Tourist Attraction (ruin, or something) Research + 30% for 24 hours, then a bunch of 1% like an asteroid holo disguise or other odd things of the sort and then some .5% chances of perm effects like +2% arti alient artifact +5% cloak .. etc) ~ like both ideas.

Miner - Mineral product +10% - Again this one needs a lot of help to ever have anyone be this guy even builders dont want to be miners
Level 200 - What black market? Passive Abiltity - Tariff for sale on minerals is dropped to 10% (aperture key lowering to 0)
Level 600 - Core Vault - 40 hour cool down limit 2 per planet Underground vault Size 1 Mining 2 Arti 1 Cloak 150 - Storage 1k of each resource ~ the Core Vault is a nice toy. The extra money and the cool building would make it a profession worth playing around with for awile, at least!

Builder - Upkeep -50% Fairly popular unfortunately but since usually the goal is to help someone who is a builder become not a builder needs some good tools to encourage people to stay builder
Level 200 - Build Cheaper - All planetary build costs are halved
Level 600 - Build Smarter - 40 hours cool down Reduces the size of an existing planet structure by 1. This ability can not be used on a planetary structure that has been modified by another source. ~ you're talking about researched structures only, right?

Governor - 3% increases chance of planetary events - meh it sounded cool .. and it might work but definitely doesn't put it in the "useful" class category
Level 200 - Official Visit everybody back to work - 24 hour cool down 90% chance that planetary production is increased by 50% for 24 hours 10% chance employees revolt and production is decreased by 100% for 12 hours ~ That's funny. I like it.
Level 600 - PLanetary Overthrow - Attempt to dislodge current government 72 hour cool down - 50% chance reduce Planetary Defense/Planetary Attack by 50% / 50% chance to fail and increase planetary Defense/Attack by 50% ~ Really like the concept, but even with the 72 hour cooldown and only a 50/50 chance, it still seems a bit OP, given that we're talking tens of thousands of attack/defense lost on some planets...

Merchant - Increases Max Cargo space by 30% - Might be the worst class needs a ton of help
Level 200 - Expand your Empire - Planetary structure Trading Hub Cooldown 40 hours - Size 1 Arti/Min/Res +1 All Production +2%
Level 600 - Now I need Protection - Ally Bodyguard - Starts at Att 80 Def 80 Hull 120 Shield 50 Ends at Att 400 Def 400 Hull 600 Shield 250 While Merchant these stats triple - Levels up everytime you create a trading hub on one of your planets ~ ooooooh

Saboteur - Have their uses - think they should continue along the same path
Level 200 - I destroy bases too - Passive - +10% Hacking Ability +10% Raiding Ability - Sabotage Base 24 Hour Cooldown Reduces Base Defense by 1% for 30 minutes This can be increased to 10% by other sabs
Level 600 - Oh wait .. I destroy everything - Sab Ship 5 minute cooldown, Can only be used on a target you have not attacked in last 24 hours (meaning this comes before your first strike) Randomly reduces Att/Def/Shield/Hull by 50% ~ that's pretty tough. I think the power needs to be reduced or the cooldown increased

Hacker - Hacking Strength 30% If your a freeze rank hacker .. you MIGHT do this .. but still needs a bit of help
Level 200 - Identity Theft - 24 hour cool down. In addition to a raid, hackers have the ability of hacking a disabled base Success based on damage done (similar to raid) RP returned based on level of base level 3 20K level 4 50k level 5 100k level 6 250k level 7 500k level 8 750k In addition , a crit hack (10% chance) will return a planet of a random member of the disabled legion
Level 600 - any thoughts for a good level 600 class ability???? ~ Technomancer: a passive ability based on your cloak/scanning power that gives you a very small chance (0.5% base chance, max -- even that might be too much) to hack into an enemy ship while attacking, wreaking major havoc: 25% chance to override shields (if shields are up, it lowers them) 25% chance for weapons overload (10 seconds with attack reduced by 75%), 25% chance to cause a reactor imbalance (massive hull damage to the ship, depending on how much energy they have charged) 25% chance dead in the water (thruster and stabilizer shutdown, defense reduced by 75% for 10 seconds)

The classes that "aren't good" need to just be removed.

Governor - 3% increases chance of planetary events - meh it sounded cool .. and it might work but definitely doesn't put it in the "useful" class category
Level 200 - Official Visit everybody back to work - 24 hour cool down 90% chance that planetary production is increased by 50% for 24 hours 10% chance employees revolt and production is decreased by 100% for 12 hours
Level 600 - PLanetary Overthrow - Attempt to dislodge current government 72 hour cool down - 50% chance reduce Planetary Defense/Planetary Attack by 50% / 50% chance to fail and increase planetary Defense/Attack by 50%

love it, very imaginative and fitting with the going flow of the game, however the only thing i can say to shoot it down is what if you switch race loads and loads to build all the planet structures and get perm effects... you would end up with some VERY OP planets.. maybe if theres tough missions to earn each ability, not sure if you meant that by the missions at the top or whether you unlock both the missions and the ability upon ranking, but yeah make a long mission a requirement for the ability, so its like youre earning an enhanced version of the profession.. works better than adding new silly races with stale ideas.