What about Avengers (the first one, not Infinity Quest)? It is more goal based rather than mode based in that you hit each character's shot/area multiple times to qualify them, then collect them, then eventually to start various "Versus" multiballs to complete them. You can "stack" the qualification/collection of each, so while it is wood-choppy in some ways, you do not realize it since every major shot is building towards a different character. It's actually fairly similar to Metallica in this way. (someone is going to get very offended that I compared Met to TAV, LOL, but the wood chop level is similar...in fact I'd say Met is choppier if you are playing for EOTL). It has a nice build-up/evolution during a long game as you start hitting the VS modes, get to the mini-wizard mode by collecting all of the heroes, etc. In my opinion, it is one of the most underrated games ever, and it's a shame so many people have written it off. It's a bear to tweak and get shooting right, but once you do it is very unique and full of satisfying shots and an interesting ruleset (especially the late game). Plus the theme is extremely well integrated, from a physical Hulk throwing the ball around and "breaking" a ramp, to the versus modes mirroring the in-fighting seen in the first movie (right down to the final shot being whichever character breaks up the fight), to the brilliant mini-wizard mode that perfectly plays out the helicarrier scene from the movie. It's well worth a second look.
You might also want to take a look at TMNT (sorry, I know it's not a DMD, but bear with me). Yes, it is heavily mode based, but it also has so many side goals that you can play an entire, satisfying game without even starting a mode. Unique skill-shots, weapons hurry-ups, Krang combos, 1-2-3 Foot combo, April hurry-ups, pizza multiball that you can change the rules of based on what "toppings" you build up before starting it, the Training system which is difficult and builds to its own mini-wizard mode, etc. Not to mention it has not only a challenge mode that lets you play Final Battle as a stand-alone game, but it also has a new speed run based mini-game, Half-Shell Challenge that is completely separate from the main game. And all that is besides the 8 unique modes which build to a mini-wizard and wizard mode, plus an ultimate mode for doing basically everything. So yes...it's mode based, but it's a very full game experience even if you completely ignore the modes.