You'll lose the 1.50 kernel support, but almost every emulator and game under the sun has seen a 3.x kernel update over the years, so you should be fine in that respect. (And in the case of emulators, newer almost always = better in any event, so there's no reason to stick with janky 1.50 kernel versions). IIRC, Gen-D3 has some sort of memory stick speed up tweak built in, a reversed version of Dark-Alex's, if I'm not mistaken.
The Gen team released a 5.50 Gen version of POPSLoader long ago, and it continues to work fine with the newest versions of 5.50 Gen CFW. I can also vouch for Dark-Alex's final release (5.00 POPSLoader, IIRC). I'd just go ahead and update the core plugin files with the Gen versions, however. The PRXes that the POPSLoader plugin's been using for years haven't really changed. So whatever you had before will still work now, though if you're missing the most recent PRXes, you'll probably want to get them in order to beef up compatibility.
I'm hoping that someone will release a new version of POPSLoader that has support for the 6.x versions of POPS. It should be more or less trivial now that the 6.x POPS files can be properly decrypted (with the release of the newest PSARDumper). It just seems like no one's gone through the effort yet.
I want to play FFVIII so bad I've almost considered buying a second PSP to keep up to date with current OFW 