It is absolutely impossible to say which of the two guys is better, as they are just so fundamentally different as players.
Comparing Rondo to Isaiah is kinda like comparing a Porsche 911 GT3 to a Bentley Continental. Both are expensive European coupes sure, but one is stripped out and tuned for a track while the other is smothered with opulent luxuries and built to pamper.
Rondo built his entire career on his ability to dominate the game without scoring. Early in his career Rondo was a genuinely elite defensive player (many people forget this), and he also will likely go down in history as one of the best rebounding and passing point guards ever to play the game. He was at or near career assist leader every year since around his 3rd or 4th year, and the things he could do with the ball were spectacular and at times almost hard to believe.
The only major criticisms with Rondo were his arrogance, and his lack of versatility as a scorer. He wasn't a good outside shooter, and that at times hurt the team and limited his ability to dominate as a scorer consistently.
Thomas is entirely different because his entire game is based around his ability to score. He's developed into a good playmaker, a good ball handler and a tough kid, but his ability to score points in a variety of ways is what makes him so dominant.
It's impossible to argue which of those guys impacted games more. They both impacted games at an elite level, just did it in different ways.
I feel like Thomas is the better guy to choose if you want somebody you can build a team around. His ability to carry a team offensively on a consistent basis makes him an excellent fit for that type of role.
I feel that Rondo is more suitable to being your #2 or #3 guy - a complimentary star on a team with multiple skilled scorers. That doesn't necessarily mean Rondo is any less a player, or that he has any less of an impact - it's just a reflection of the fact that he isn't a pure scorer, and so being a #1 guy doesn't really suit his game.