That is quite a mismatched group of fish in the tank currently, I can see why there would be an issue keeping guppies and other livebearers thriving in that tank. Dwarf puffers, while small, can cause quite a bit of stress and physical harm in chewing on other, more peaceful fish, even ones bigger than themselves. Siamese algae eaters, as they mature, also can get quite aggressive and will hunt smaller, weaker fish. Peacock eels are predatory as well, and if it fits in the mouth it is potential food. Considering they average about 6 - 8 inches long in home aquaria, they have the potential to grow to 12 inches.
Your take on mixing loaches into that tank once the livebearers are gone is correct. Too many bottom feeders that will need to fight for territory and food in a small environment. Not a good idea.
You didn't mention your plans for the dwarf puffer? Is it to remain in this tank? That will make a big difference as to what can be kept in there.
Angels for a 25 gallon? Nope.
Minus the puffer you might want to consider dwarf gouramis instead of standard. They would be better suited to that size tank and should still be able to hold their own against everything else, just don't mix a bunch of males into the same tank or they will fight. If you could get a pair of same species dwarfs, that could be a great mix for you and offer a mid to upper dwelling fish. Be sure with gouramis to add decor to the upper level of the tank so they have shelter where they need it. Tall plants that reach the surface or lay slightly over the surface, or floating plants all work well. They don't have to be live plants to work, as long as it breaks up the big open space. If you have plants down below be careful not to shade them out too much from the light.
Other ideas, without the puffer and without gouramis would be things such as tiger barbs, rosy barbs, odessa barbs, cherry barbs, gold barbs, most barbs would work well. Watch odessa barbs, make sure they're big enough to not become eel food before introducing them. All of the barbs I listed can be mixed, so a small group of 2 different species would make for a pretty mix. (a male/female pair of each can be very pretty) Be careful not to over stock the tank.
If you need more suggestions let me know, I can think of a lot of possibilities.