I own and like both these games. So as far as these two games go, neither is really deep, in my opinion. However, if I had to rate one on depth vs the other, transformers wins. As far as fun, Tron probably wins. Transformers I'd say is deeper because you will need to play for a very long time and accomplish a crap load of stuff to actually beat it.
In tron, you have to light each of the center lights up (tron, clue, quorra, gem, etc). You have to do certain things to get the mode started, then complete it. The ball times are extremely short. The game is a fast game, good for two player. Game times are very short and quick. The flow is really good, the upper flipper adds a lot to the game. There is a lot of randomness to Tron and you will not always have control of the ball. The game forces you to take shots that will result in a random ball return even if you make the shot. The game is very difficult. You may hit sea of simulation often but not portal. So far, none of us have gotten to portal yet. (And we are not total dumb players. We have all ruled the universe in AFM, beaten CV, TOTAN, and several of our other games).
Transformers is not nearly as fast paced, but still pretty quick. The LE moves much better due to the orbit shots that flow. The ramps are a little slower but not much. The orbits really make the difference vs the pro. In any event, in TF, the rules are the same. You hit the lit shots until a mode starts, hit more lit shots until you complete the mode or your time runs out. Light all the mode lights up and move to the wizard mode (sentinel prime for half way, battle for cybertron for end). I've gotten to sentinel prime a couple times, never battled cybertron yet. Ball times are long. I've had 30-40 minute games in TF. Longest game in Tron was around 10 mins. Transformers is not a good multiplayer game. You'd be waiting for your turn too long.
As far as theme, I'd say that Tron implements the theme better than Transformers. Both have excellent sound and adding a sub and shaker really enhances both.