For our anniversary, I got my wife an imported copy of Doctor Who: Evacuation Earth for the DS. Before you call me Homer Simpson giving Marge a bowling ball know that she specifically asked for this. Unfortunately, she gave it up pretty quickly as soon as she discovered the game was really nothing more than a Brand X Professor Layton. I lasted just slightly longer than she did. What kind of crap Doctor Who adventure gives you a sonic screwdriver at the get-go, but makes you look for a lock pick?
1. You Have a Protagonist That Can't Kill Anyone
The thing that has always made The Doctor different is his dislike of guns and his refusal to kill people. Sure, sometimes that's not exactly a good thing. After all, he let the Family of Blood live, but trapped them in the kind of Hells that make Dante look at Hieronymus Bosch and say, "I wish I'd thought of that." And yes, despite his moral code The Doctor has in fact killed many living being, sometimes just to casually prove a point.
Those lapses, though are lapses. If you focus on them you get something like Dalek Attack which is basically Metroid starring The Doctor, and thus misses a lot of the point. Seeing as how even the most family friendly of games like the Mario series are still at their hearts one long progression of murder, that leaves not a lot of action left that The Doctor can do.
2. Creating Puzzles That Make Any Sense Plotwise is Really Hard
If The Doctor can't kill someone, then just make the game a puzzler. Simple, right? Well, there's nothing wrong with that idea except that making a puzzler that isn't ridiculous is actually very hard.
Remember how I mentioned Evacuation Earth? It uses the exact same system as Professor Layton and those are great games. What's the problem? The problem is that Professor Layton games are about puzzles. Ninety percent of the games are "That reminds me of a puzzle" with the plot being mostly secondary while at the same time just another puzzle. Or take something like Portal, where puzzles are the M.O. of the antagonist.
Pretty much any other puzzle game has to use ridiculously contrived conundrums in order to pad the gameplay, which is how you get the aforementioned looking for a lockpick when you already own the ultimate one. Which brings us to...
3. The Sonic Ruins Gameplay
The Sonic Screwdriver in the classic series was at one point so ridiculously overpowered that producers had to break the thing just so lazy writers would stop using it to get out of plot holes they had dug. You could argue that in the new series the same problem occurs a bit, though you could say the same about the phrase "deadlock sealed" in order to wave away reasons why the Sonic doesn't work in a given situation.
That's the problem with the tool. If The Doctor doesn't have it in a game, he's not the Doctor. If he does have it, there is no progression of abilities because they are already ingrained. It's bad enough that Batman has to retrieve his stuff one quest at a time in the Arkham games, but at least they are different items. The Doctor only has one because The Doctor only needs one.
You can use a puzzle mechanic like Eternity Clock does to add some excitement, but it really does feel forced. In short, the Sonic itself is a roadblock to the necessary accumulation of superior skills which is the basis of all adventure games.