I still don't have legacy yet and currently use TMCC, but when I buy a Legacy locomotive, my dealer, does a full unboxing and thorough checkout with legacy in front of me free of charge.
This makes sure the locomotive I go home with is fully operational and should work when I get home. Once I get it home, I use either TMCC or conventional knowing that the last time it was checked out with Legacy, everything worked properly. Plus it gives me an excuse to play with Legacy in the store for a short time.
If you are worried that all the features won't work under Legacy, have the dealer check it out for you when you go pick it up. Most will be happy to do it. Then when you eventually do get legacy, you at least now everything worked when you purchased it.
I would not let it delay my purchase of a locomotive just for not having the command control.
Also, for some reason, eBay has some very ridiculous prices of the 990 like someon mentioned, probably because many dealers are waiting for replenishment from Lionel, but don't overpay for it. You can always order it from your dealer and when it comes in, you won't be ripped off. Most dealers will have sales, coupons, or a discount off MSRP. Just need to wait for it to come in stock or call around.