Both have been on the market for some time and have a quite a following. I have no experience with either but I run an FT-710 which is kinda the baby brother to the FTDX10 and I'm happy with it. It's Yaesu's first fully SDR radio. The FTDX10 has more front controls versus menus and a little bit better filtering. The 991 is more portable if you're looking to go in that direction and don't want to spring for two radios at this point. Either way, they're both solid choices.
Antenna wise, I'm more of a builder then a buyer. Simple inexpensive components and some wire and you'd be surprised what you can do. No experience with a DX Commander but from what I've have seen and read, folks like them.
Andy
KC3WRX