okay, after a lot of trial-and-error I have started playtesting a ruleset that I think does what I want it to do... I'll share it with you, but since it is very much work-in-progress, don't expect it to be perfect.
I'll try to sum the included changes up tomorrow, but right now I'm just going to throw it at you in case you want to try it
EDIT: added "Tank Weapon" name strings
EDIT2: okay, a try at summing up the changes:
1) you cannot use the plasma weapons after researching them: the alien guns use a thought-activated trigger that only reacts to the brain-waves of the designated user, and we don't understand the circuits)
2) once you researched one weapon
and its clip (small launcher/stun bomb and blaster launcher/blaster bomb qualify, too)
and alien alloys, you can research "alien weapon technology"
3) research of "alien weapons technology" gives you an insight in the trigger mechanism: you can now retrofit those captured weapons you already researched (again, need to have researched weapon and clip) by simply bypassing the thought-activation mechanism. you can use the retrofitted versions, but they are less accurate and use more TUs. oh, that doesn't work for the blaster launcher, of course, that one is too complicated
4) once you researched "alien weapons technology
and "mind probe", you can research "advanced alien weapons technology"
5) "advanced alien weapons technology" shows that the mind probe can be used to emulate the thought-trigger functions. you can now produce your own versions of the alien weapons (those you understand)
6) to manufacture an alien weapon, you need one mind probe per weapon as a base material, to manufacture the trigger system (because we just aren't capable of creating the circuits, just use them)
7) once you researched one
plasma weapon
and its clip
and elerium-115, you can research "elerium plasma technology". this enables you to replicate the plasma clips you already researched. also, once you researched "advanced alien weapons technology", you can manufacture the human versions of the plasma weapons you understand.
8 ) blaster launcher
and blaster bomb, once researched, allow you to research "elerium fusion technology", which then allows you to research human blaster weapons
9) for laser, plasma and blaster weapons, the craft weapons and HWP weapons have been split up into separate research subjects.
10) speaking of HWP weapons: I added tracked HWPs with plasma and launcher turrets, and hovertanks with laser cannons, because why not? (haven't tried them yet, though, so I cannot guarantee that they are working as intended
)
11) having researched "alien alloys"
and "elerium-115"
and "ufo power source" allows you to research "elerium gravity technology"
12) "elerium gravity technology" gives your techies the knowledge of how to use of elerium for creating ellipsoid gravity fields: this allows the research of "new fighter craft" (aka firestorm), "new fighter transporter" (aka lightning) and "hovertank", all of which are seperate independent research projects now.
13) "elerium gravity technology" also allows research of "advanced elerium gravity technology", a really long project (2000 research points needed): this gives you the knowledge of how to create gravity fields of other shapes. this allows research of "flying suit" and "ultimate craft"
...I think that's just about it. again, this is work in progress... as I was writing this, I discovered several flaws in the .rul file, so it is now again updated
EDIT: found some more flaws, especially in my modified tanks not being defined as units, resulting in all kinds of crashes. ruleset updated