I've been thinking much along the same lines. I've been tinkering with my own personal Ruleset(s) ever since the wiki page showed up. I actually finished planning out what I wanted to do in terms of tech-tree rearrangement yesterday, and the OP and I seem to have some similar ideas. Here's the gist of what I've got;
Just to be clear, a major goal was to make Plasma weapons extremely special. Beyond making them harder to research, I removed the ability to manufacture them, and intend to play with the 'alien weapons are destroyed on death' option on. So basically, captured plasma only. I did add an extra tier of weapons to offset this (railguns), but they still aren't as wildly effective as plasma weapons.
As for research, the pertinent part of what I've got planned and hope to playtest sometime soon:
- Everything, except the Motion Scanner and Medi-kit, are locked behind either Alien Alloys or Elerium-115, if not both.
- Laser Weapons require Elerium-115. (This makes it about 3 times longer 'til you get Laser Weapons if I read the ruleset right; It also puts them on the road to better craft, but what can I do?)
- Any captured engineer, once researched, will unlock Plasma Theory and the UFO Power Source.
- Plasma Theory is one requirement for Plasma weapon unlocks; It's also a prerequisite for my Railguns.
- UFO Construction no longer requires UFO Navigation (furious handwaving about making do with earth radar or something)
- The Lightning project now comes before the Firestorm project, which sort of 'forces' its use.
- Firestorms DO require UFO Navigation which...
- Snakemen or Muton Engineers (and the apparently-theoretical Ethereal Engineers) unlock UFO Navigation and, along with Plasma Theory, allow you to finally be able to research those captured plasma weapons. (This is pretty much a straight-up gamist make it rare/later in the game type thing)
- Plasma Weapons follow the Laser precedent of Pistol unlocks Rifle unlocks Heavy (as Gifty suggested)
This is the gist of what would be pertinent to the base game, I think. I haven't messed with how long it takes to acquire techs as yet as I want to see how there being a more complicated tree affects the pace of the game.
I hadn't thought of making the Mind Probe be a prereq for interrogation, and it's an idea I'd love to steal. I considered getting really nasty and requiring any alien corpse research to unlock the Alien Containment facility as well, but that might be a tad much.
Another idea I toyed with (but ultimately decided against) was to require Alien Medic research for a set of more effective versions of Earth weapons, based on the idea of learning more about alien physiology.