I think customisable ships would be a big improvement, as it would force strategic designs and it would give players the definite feeling that there ships are growing considerably stronger(which barely exists at the moment, i.e. cap ships available from the start, 10% or 5% increase in damage per tech level).  This would make  early ships being no match for upgraded ships, thereby forcing investment in advanced technologies.
Such as:
More customisable weapons, do you want to focus on mass drivers, laser, phasers, torpedoes, missiles, or the killer nerf beam lol.
At the beginning no shields - must be researched and have clear advantages at higher levels - such as completly nullyfying earlier game weapons or specific type of weapon.
This could be similarly applied to armour types.
Research in new weapons tech showing much more improvement in damage output, or armour/sheld piercing weapons.

I for one like the idea of watching in horror as a massive fleet phases to my main deensive choke point, and fearing certain death, realise that the fool has spammed loads of early ships in an effort to overwhelm my forces, and I cheer with delight as my fleet which is 1/3 of the size, consisting of highly advanced frigates and cruiser completely wipes the floor with his primitive vessels.
I don't know if this would completely hang the most powerful systems (im not expecting reatime galciv) but heres hoping!

P.S. Love the game already though, but I also love the idea of clear technologial advantages, with tech breakthroughs changing the tide of wars.