haha I spend hours thinking of this 
Balancing weapons is sort of why I created my mod, although it only has alloy ammo and delayed lasers. Currently everything else is up to the player, by using other mods (laser tech tweak and Plasma needs Elerium). I am considering a system which would leave "anchor points" to be used by modders to "latch on" with their mod, but making a stand-alone and compatible mod is tricky.
Back on topic:
Here is how I see the weaponry progression with current mods:
1- Conventional weapons (with some added stuff like grenade launchers, flamthrowers, shotguns, etc)
2- Alloy ammo (fits in conventional weapons but upgrade damage)
3- Gauss and Laser Weapons
4- Elerium based lasers
5- Plasma and Blaster Launcher (the real endgame weapon, and I think that shouldn't change unless aliens come up with something better).
As I suggested above, I think using DE ammo to "upgrade" Gauss weapons to a tier4 weapon would work well. Since it is based on depleted Elerium, it can't really be better than plasma. It could be another upgrade to tier 1, but new ammo for basic guns is already done, so that's kind of boring.. Of course, upgrading Gauss is kind of niche (but it would work in the FMP, and I am also starting to use Gauss, so would work in the XAE too).
For armor/tanks/crafts, I really don't know.. If DE is better than Alien Alloy, it's increasing the upper power limit and that's much more work if you want to keep things balanced. It could be interesting though, and I know the "Equal Terms" mod is supposed to introduce new alien weaponry in a later version, so you could balance it with that.
You do bring up an interesting notion. Adding tiers to upgrades. I'm tired of seeing Plasma at top tier...it needs a terran developed alternative thats related. Building a physics research tree that allows exploration of an alternative is good. I'm working on a mod that sort of simulates this.
Few things:
1. Depleted Elerium is better off being produced instead of found. A mod that creates 50 units of depleted uranium from 10 units of Elerium and 1 unit of Alien Alloy really fits the bill.
(The aliens have been working with Elerium for several millenia. They've learned to consume elerium at the highest efficiency, leaving nothing behind for waste. We have no problem with waste, and we specialize in turning garbage into deadly weapons to kill humans. )
2. Depleted Uranium is used as an weaved metal alloy for component (Chobham) armor on tanks. Its a game, and I don't want to over analyze something thats completely fictional, but again, as a resource that can be created by man, I can see such a use.
3. However, again, the tough part is finding a strategic "tier" level for it. What technology would it compete against? We all can't see the value of Elerium toothbrushes, and Alien Alloy bicycles. Just applying everywhere does not make it useful.
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