I had an idea about a bonus for ship allies. Basically its an idea for a synergy bonus given for having certain ship allies. For example if you had both Seh'rin and apparitious, you could get an extra bonus to a particular stat. This bonus of course would not be affected by the ship ally percentage bonus, its just an extra bonus for having both of those allies. There could also be a different bonus for having Anubix and Vortov, or it could even be a combination of three allies which would give the synergy bonus i.e Seh'rin, anubix, and apparitious. Not sure what anyone thinks, but it seemed interesting so I thought I'd post.

+1 would give more incentive to get certain allies

The existence of the Allies is incentive enough to get them.

I think a better suggestion would be if there comes a point where more allies of the same "type" are introduced then have some synergy bonuses factored in ..

ie

A chain comes out for the Crimson Blades that ends up introducing 2 new allies a mechanical and a mercenary..
Individually the anubix stats wise would be better then the crimson blades mechanical ally and vortov would be better than the crimson blades mercenary ally..

But if you level both crimson blades allys up to 100 while both are equipped a certain bonus/ability is given to your ship that might make it beneficial to have both crimson blade allys installed..