I have heard this game plays best with all six races. Not having the luxury of that big a board game circle, will this game have the same feel if players play with multiple races (aka, player-to-race ratio: 1:3vs1:3, or 1:2vs1:2vs1:2)?
Players Playing More than One Race?
Some people play Dune one on one with three factions each. There are even variants where the factions may randomly change sides at a nexus (Temporary Ceasefire in Rex). I have never played it this way, and maybe it is somehow fun, but I doubt it is as fun as a game designed for two.
Three-player may be fun enough just playing by the rules. I was surprised to find that Rex is fun with four. If I get the chance to try it out with three soon, I will certainly report back, though Ascension has been our go-to 2/3p game of late.
Like Adam said, there are rules for playing that way if you look at Dune variants available on the web. They'd probably work fine with Rex as well. That said, I don't think a three player game with each player playing two races would be any better than a three player game with each player playing one.
As has been said in other threads, the magic of this game is the human interaction that players bring to the table. Bluffing, lying, scheming, general diplomacy. The reason its best with six is not because of any mechanical reason, it's just because six players means that many more vectors of intrigue bouncing off one another.
I also think playing with multiple races per player would be cumbersome. You would still have to keep influence, cards, tokens, and leaders separate per Rex rules. For a three player game, if it isn't fun by standard rules, what you might could do would be to give each player the alliance ability of an unused race. Lazax and Letnev and Sol should be main players as their alliance abilities would do nothing (well, next to nothing for Sol, and they are kind of key to the story). So perhaps it could go like this:
Lazax, ally: Xxcha
Letnev, ally: Hacan
Sol, ally: Jol-Nar
Hacan and Jol-Nar should not go with Lazax as either would be too powerful a combination to have throughout the game. Letnev + Jol-Nar might be too good, too, as that's a whole lot of battle prowess. I think this might be the best balance, theoretically. Sol-Nar synergizes with Jol-Nar quite well, but I find the Fremen to be a bit weak in Dune and haven't noticed Sol to be a huge improvement yet, so I think that works.