SC2Mapster

Since there are "Dark Protoss" models, you could kind of make 2 variations for missions where you choose between the normal and dark toss (Like the mission where you choose Tosh/Spectres or Nova/Ghosts) and will then be using the either normal or dark version of the unit that was unlocked depending on your choice for the rest of the campaign. You'll have to do something to make a difference between those units though
Maybe make "Dark Zealots" instead of having charge, have something like a 3 second cloaking effect, make the dark stalker do more damage but have less health, have the Dark Sentry and Dark HT have different spells, etc.

You can basically keep the concept of the armory, just convert it to protoss upgrades.
Mercs... Now that one is hard :/ Maybe if you use my idea of choosing between dark and normal units, allow the other type to be warped in just like Mercenaries in campaign with large cooldowns and limited uses?

For Research.... hmmm... I guess you could still keep the research thing, but i dont know how to convert it to fit protoss... I mean, for zerg you could make it that you acquire DNA during missions and can evolve that way, yada yada, but toss... Seriously no idea.

Here are some random ideas for upgrades/Researches:
Warp Prism - Power field increases to that of a pylon and/or let it generate power while moving
Make Warpgates an upgrade you have to buy (do that for most of the stuff that's researched in-game. Blink, charge, Storm, etc.)
Stalker - Increased damage vs Armored and/or longer range and/or increased health
Zealot - Charge, and i dont know how to do this, but lorewise zealots become immortals after dying, right? So, like the "immortality protocol" for the thor, make something similar for zealots and immortals. Or that you can only build immortals after you lose zealots (so each zealot you use = 1 immortal you can build)
Nexus - Power field? AoE Chrono boost?

I'll think of more and edit or post again.

For mercs you could have it be alliances and have it bring in a protoss leader and some of their band (think the last protoss mission from that memory thingymagig) or even bring in terran units (Raynor seems to help them out a bit).

Someone in the art forum made a reaver model. You should definitely add that.

Dark toss arent necesarily evil :p look at Zeratul

But what i meant is not that you choose to convert a unit, but like in the WoL campaign, almost every mission you get a new unit. First it was marines, next it was medics, etc. Do the same here, just that instead of getting a specific unit, you can choose whether you want the dark or normal version of it (and then you stick to that version for the rest of the game). Kinda like the choice between spectres and ghosts...
and you don't have to do that for every mission - there are some units that simply don't exist as dark, or some you just don't have to offer. Also, maybe make a choice between HT's and DT's - then give DT's some badass upgrades that can be bought to make them worth it.

And i just got an idea for research... Again, tehre are Dark and normal toss. have 1 Dark tree and 1 Normal tree (like there are toss and zerg trees in teh WoL campaign), then you gain research points for helping certain tribes, or maybe even get research points for using certain units (lets say you warp in 10 DTs in one mission = 1 dark research point (only triggered once, 20 DTs wont give you more points))
Have the dark tree specialize in stuff like cloaking and damage, and the other tree in other stuff

as for currency... I have a kind of idea... Lets say if you choose to have Zeratul as your main guy (like raynor in WoL), lets say that lore wise instead of warping units in from Shakuras, you get them from a place of your own.
Now, logically seen you need a power source, right? And the bigger and more upgraded units are, the more power you would need to warp, right? So just instead of using an actual currency, make it like warp-power capacity, which is increased by some crystals that you gain during missions (people who "hired" you give them to you, etc.). Then for mercs, you can use other tribes, but they'll want the crystals, and if you're gonna use Raynor (which is a great idea) you give him the crystals so that he can power the hyperion (and give stetman something to do)
Also, another idea i had, which is a mix of the raynor and other tribe idea for mercs... Have toss units with some terran technology. Zealot with the firebat attack? DT's with Jetpacks? Stalkers with... uh... no idea for stalkers... Siege mode immortals?

Also, if ya need help, i'll try and do stuff with ya :) Can't promise too much time, but i'll definitely jump in for story-writing, and maybe some data or trigger work (preferably triggers), if you wanna know how good im with data, DL and play my map (danger - could be buggy) Gates of Darkness, or just check out the data editor after DLing it.
Reason i want triggers is because i find them easier and less time consuming than the data editor xD

I think keeping the in-between missions area would be better. Yes, if you look at the hyperion its got craploads of triggers that are a crapload of work...
BUT, first of all, you dont need to actually have all those characters AND remember, you make those triggers progressively. You'll probably just need to make a couple of triggers first for the halos and loading the banks and the interfaces, and after that you just add a couple of triggers after each mission you make. I don't think it's that much work, or at least not as much as it seems.
And you could also keep it simple by just making it a protoss base on some planet/spacestation/Whatever, and not add any rooms but just have the forge for unit upgrades, a nexus, pylon or the voidseeker isntead of the starmap, some random protoss guy for mercenaries (or a computer connected to the hyperion if you're gonna use any of the ideas for mercenaries that involve Raynor), a cyber-core for research, and have Zeratul standing somewhere to give you updates on the story (or just have him stand somewhere and do nothinhg or walk over to whatever object you click)

And @ your comment at the trigger things
I know how to do abilities in triggers in WC3, but every attempt so far in the GE failed, lol. So i was forced to learn to use the data editor, which i find simple enough but just time consuming. If you need any complex abilities, i think i can do a lot of stuff, but i can't do anything advanced with actors :/