Just came today to these forums since I was bothered by exactly the same things as the OP.
However I'm not so sure if this is a problem or not.
I believe we have 3 issues:
1) Terrain - tiles from expansions are only used in the scenarios from expansion. Never will tiles from 2 expansions be mixed together.
It might not be true. The tiles are numbered, like 43A from LoR. If future expansion needs such tile, it can easily be also present in this expansion.
This means that if some player buys a lot of expansion he might run into having more than one of each piece which isn't necessarily bad. We also have a quest vault where we can build multi-expansion scenarios.
Also FFG could release multi-expansion scenarios that are only for players that have all of them or some set of them.
a) From hero perspective, it is not a problem as there are a lot of abilities: Choose 1 condition. Target suffers that condition. Plus there are items in each expansion that use certain specific conditions and heroes will be able to obtain them. The more expansion are there the more items in shop decks, but the more we have options of "searching" through the deck to find what we need.
b) from OL perspective he always has access to all conditions through the open groups. However, no new monsters will burn, which is thematically strange.
But this could also be remedied, by introducing alternative lieutenant and monster cards. Or just monster and hero packs that would require certain expansions.
Also there could be, that some expansion in the future will again re-introduce burn. No big deal.
OL could also get abilities where he can choose conditions freely, just as heroes.
3) Dice - this is not a problem at all, since from Labirynth of Ruin each expansion will contain green dice. It is also not expected that some expansion in the future would introduce another die. And even if it is so, the cost of each expansion would be increased by 1 die. Not a huge cost, so no problem.
That said, I see a problem in the Lieutenant decks design. Lieutenants SHOULD/MUST be tied to the expansion they came from!!! I also don't like how some Lieutenant plot decks are ignoring the core rules that were brought by expansions. For example Belthir ignores the fact that there is a Basic II deck in LoR.
IMO this should be re-thinked by FFG.