Ya, I understand the dilemma. It's amazing the ships that I haven't found a place for. But for the most part I've found a way to use nearly every one that I deemed a must have.
There are a couple of things you can do. Conversion to a 1st generation X-ship is one. The process is easy to follow and can be adjusted to taste. It's also useful as many of the ships you are interested in are of an advanced design. Another option is making a 'Fast ' variant. All you need for that is to increase warp by 20%, to reflect the hot warp engines. Then replace half of the heavy weapons with main phasers of the same arc. Easy, no? That is one of the ways I used to specified some of the FASA starships.
Another way to go is to make a one of a kind variant of an existing specification. A simple change like converting APR to warp reactors or replacing half of the hull with armor on a one to one basis. Or just add the armor to make it an armored variant. Think ablative armor. This way you don't have to feel like you are corrupting the fleet library so much to find a place for something you just have to have. So long as you pay the BPV for it, it isn't necessarily unreasonable. Some of my favorite self made ships are of an early, low tech, type. And when it comes right down to it, they are just as much fun to fly as the mega-uber ships. Perhaps more so.
Another thing I have done is to make a carrier variant. It's very easy to add a couple of fast patrol ships to a given specification. It also is easier to swallow as all you need is a mechanical link to dock it to. Check Firesouls's OP+ Shiplist. The Lyran's did that to most of their ships. Or perhaps a 'command ' version. A little more bridge and a special add-on perhaps as innocuous as a couple of special sensors. In Starfleet Battles it was legitimate to make modest changes, as the rules permitted, to balance a skirmish according to the starships BPV.
Where there is a will, there is a way...