Naquadria is admittedly a very powerful. If you know what you’re doing (and have 300 Thorium to spare), one rod can perform similar to a ZPM, both in raw power output and time it lasts, however since all the output is in HU, the infastructure to convert it to EU is quite significant and also loses half the energy. I don’t think fission having potential to be this powerful is an issue, but it may be a bit too easy to archive right now. Such reactors will also probably have the potential to erase your whole base when fission explosions get enabled again, fusion has the benefit of safety.
My proposal to make fusion more relevant would be to gate enriched naquadah and naquadria behind it and removing all other ways of obtaining it. Fusion, while having some energy production potential, is probably best used for high tech material processing. Using a fusion reactor to turn Naquadah into Enriched Naquadah seems somewhat logical. Naquadria can stay as a fission waste product from Enriched Naquadah, since converting the Naquadah this way is no easy feat. Since Enriched Naquadah and Naquadria are (to my knowledge) only useful for fission anyway, this would be a great way to tie fission and fusion together.
The concrete recipe I’d suggest would be Naquadah plus Plutonium 239 resulting in Enriched Naquadah plus Lead plus Helium and/or Hydrogen (isotopes) to balance particle counts. Having to use a fission fuel in addition to the Naquadah gets around the issue of Naquadah being able to be produced with the matter fabricator.
Speaking of the matter fabricator, something to produce QU that isn’t the ZPM could be useful, since otherwise you are limited by a T5 Quantum Energizer only being able to supply 4096QU to a matter fabricator, since there are no “quantum cables”, which would probably be a niche an Aneutronic Fusion Reactor could fill.