If you can afford a bedroom, by all means get it. Far more room than a roomette, especially for two people. And a decent private toilet (and shower) with a door. In a roomette, unless you know each other really well, one of you is going to have to step outside while the other uses the facilities, and in some cases you might not want to rush back in. I travel solo a lot, and will miss the individual toilets in the roomettes, but the one silver lining is that every car will have public toilets.
I've done that long walk to the first coach toilet many times. My co-traveller appreciated it. But I always felt guilty opening the coach end doors in the middle of the night and waking up whoever got stuck with the coach seat nearest the door and toilet.
Re upgrades, in the old days an upgrade could often be "arranged" by a small fee to the SCA. On a recent LSL trip, I noticed some bedrooms available for only a few dollars more than I had paid for my roomette (has to do with bucket pricing), and the conductor was helpful in arranging it but it took him about 15 minutes to change my ticket, and he had to make a phone call to reservations. He even asked for my Amtrak telephone pin number (different than password) so he could make the change for me.
p.s. This is talking about east coast roomettes with individual toilets. On west coast trains roomettes don't have toilets, and everyone goes down the hall. Unless you're by yourself and have a bottle...