Joel_Katten: a lot of the equipment has to be either bought from special places or found as loot, the federation vendors won't really sell much beyond whats standard issue.
I suspect the earliest you'll see anti-proton or tri-cobolt would be mk 7, though if your lucky chroniton can be found at least at mk 6 (assume mk 5 as well) along with the transphasic just have to get some lucky drops.
vf1sveritech: I've heard that as well but I also heard they scrapped that idea at some point, granted the weapons may do more damage due to mob resistance or their procs (disruptors resistance debuff will be for hull damage, and phasers can disable a shield), I'm afraid I wouldn't be able to confirm nor deny whether they have or not...
ErinStarbuck: the high yield plasma can be lethal if used at close range so they havn't gotten a chance to shoot it down, it can be more effective then most other high yields when used right, the down side is that your normal shots are not going to be that much better then photon torpedoes.
Hunsi.Kanzo: According to the dev's this is a bug and they should still be on the weapons, even if they don't show up on the tooltip. hopefully they will fix that soon.