Indy was installed at DL long before Disney owned the franchise. Also, Disneyland does not have as many options as WDW to choose from.Wrong. There's a whole expansion pad in MK south of Pirates. It also seems to be just fine in Disneyland in California and Paris. It would work fine in MK too.
Not to mention with the horrible crowding SWGE is going to bring, DHS needs all it can get to spread out those crowds.
My guess is that now that Disney owns the franchise they will want to feature It with a much bigger land than what you see at Disneyland or Paris or the available expansion pad in the MK.
Putting Indy in DHS might just be too much of a good thing for that park.
Time will tell and I am sure they will choose wisely.
See what I did there?