Okay, this topic seems touchy. I'll bet I'm in the minority when I say I don't want heroes the way Endless Space had heroes- but let me qualify. I think the ship EP system should expand to cover those roles. For a start, each level they gain should bestow more than mere hitpoints- a gradual improvement to weapons and defenses, an added automatic repair during combat, and, at higher levels, the addition of special bonuses to the ship. Having the ability to choose between the upgrade path would help here, but the net concept is that your military should naturally generate your heroes over the course of battle.
Ships slowly accruing special abilities seems more realistic than some dust-addled dimwit adding huge bonuses to ships he's not currently standing on, as in Endless Space, not that I'm knocking it. I just think this is better, and will add a bit of heart to those little digital ships scurrying about to conduct your imperial business. They already leveled up and gained HP, but that was very bland and gave the fleeting system bugs. Independent EP calculation slowly making battle-hardened steel citadels out of soft green nugget flesh also adds to the battles, where you can root for your insanely-lucky ship as it rampages around becoming a boss.
I am hoping for a lot more ship development over time, and some big dollops of awesome in the ship design system. It would be wonderful if these areas had some TLC during the pre-alpha phases while ideas are being integrated and smoothed off.