The non-fleet upgrades are indeed wasted resources, the fleet retrofits are definitly not. Looking at their stats they may have lower shield mods, but all T2 and T3 fleet upgrades get additional shield capacity outside of their shield mod. The only real difference is natural shield regeneration (which depends on shield mods), but capacity is comparable to T5 fleet upgrades.
Example: My Fleet Nova with Maco MKXII and without Field Generators actually has a slightly higher capacity than my Fleet Nebula. T5 fleet upgrades will have higher capacity as soon as you start to add Field Generators, since again T2 and T3 have lower basic mods.
Hull values aren't an issue at all and you can't compare a Nova's hull and a Deep Space Science Vessel. The Fleet Science Vessel Retrofit is basically a Recon variant and with this it is on par. The Fleet Research Science Vessel could best be described as a D'Kyr fleet version without the questionable pet and with an awesome turn rate.
I can't say anything about the Fleet Escort Retrofit, but I can assure you that the Fleet Science, Fleet Research Science and Fleet Heavy Cruiser are all excellent ships, even for premade PvP. Same goes for the KDF ships.
I think I see what you're saying. I see the sense in comparing the Fleet Science Retrofit to the Recon, in fact I'm comparing their stats side by side right now.
The only straight up "better" things about the T2 Fleet Retrofit are the +1 Turn Rate, and the Lieutenant Commander Tac Boff slot. That's not really a lot. Otherwise, its up to preference: Engineering console vs. Tac console, etc. Otherwise, you get almost 2,000 more shields, 2,000 more hull, more crew....and they're PRICED THE SAME?
Compare also the T2 Fleet Escort Retrofit to the T5 Fleet Patrol Escort, and we have the exact same problem, perhaps more drastic. In fact, the only reason the Patrol Escort isn't a straight upgrade is 1 point of turn rate.
I don't want to seem like I'm overreacting, but I don't feel like the 1 extra turn rate and the Lt. Cmdr. Tactical slot warrant such a huge difference in shields and hull. It would be balanced much better if the Fleet Science Retrofit had a shield modifier of 1.43 and 29,700 hull. It'd be pretty close to the Recon Science Vessel, with some preference differences: Science vs. Tactical, Consoles, etc. Balanced by turn rate vs. crew and stuff.