Ok so here is my idea - let some of the long research chains have an additional bonus at the end.
Something that will reward a person who decides to focus on this one research line. Something that'll make it slightly more worthwhile to go 'all the way' than just yet another '+5%'.

For example: (examples in Vasari techs, of course should apply to all races in their own way and style)

• The final "+% hull strength" upgrade could give an additional "+0.5 armor" per level of the upgrade.
  reasoning - when the hull receives so many enhancements for controlling damage, some hits that were threatening before now become merely scratches.
• The last culture upgrade could give "+5% population growth rate increase in friendly culture" per level.
  reasoning - oppressed population is so heavily brainwashed that it begins to enjoy the careless life, without having to bother with stupid piliticians trying to convince one another that their lies are better for the future of the galaxy.
• Final trade upgrade might give "+20% to trade ship replacement rate" per level.
  reasoning - when a tyrannical empire focuses so heavily on trade, every single individual charged with supervising the flow of merchandise feels a strong pressure to do his best. Factories struggle to maintain the fastest possible construction speeds so as not to anger their rulers.
• Final upgrade of Wave cannons might give "-5% antimatter regeneration rate for 10 seconds" per level to Enforcer's and Cap ships' wave cannons. Affects enemy frigates, cruisers and caps.
  reasoning - heavy wave cannon barrages cause electromagnetic shocks that ripple through the enemy ships' hulls and disrupt antimatter generation and storage systems.

and so on.

It's not the ideas above that are important nor their balancing, but the very idea of giving some other bonus to those end-of-the-line researches. To make them more appealing and open the possibility of new tactics to be employed.