My secondary base is pretty far along on prestige upgrades. All offensive buildings have been long done, all shields are done, and I'm on my 9th turret. I'm about to run out of level X turrets, so I'll pick up the remaining storages until I get a fresh batch done. This base was a mini with two turrets until ~last february, when cnfo forced me to build it up (was gonna happen anyway).
I'll be upgrading my main base to Presto in a few months (could do it now, but don't feel the need). IMO, there are really on two benefits to going prestige: Upgrading transports to get to 132 UC in the loadout, and upgrading the shields. The shields go up by 10 K in health (going from 9 to 10 is less, only 5.5 K), and they get extra range, which is huge to me. So, my strategy will be to first do the research center, then do the transports, then 2X alloy storage followed by the four shields. After that, I will probably do 2X credit storage and then upgrade my star command, because I will want to have the ability to take out shields with Tie Advanced. I've been sitting on over a hundred samples of Tie A's/stolen A-wings for what seems like forever, it will be nice to be able to finally use them whenever I want.
After that, I'll do the normal offensive buildings, and by that time I will have a lot of troops and vehicles upgraded to presto (I won't still be chasing level X upgrades by the time I make the move to presto). To me, prestige troops aren't that awesome, anyway. Level X with the skins I have (almost all level X) work plenty well.