D&D has enough bonuses and penalties to remember and add to every roll. I wouldn't want to add another one, especially one that lasts several days of game time and applies to a different attribute every time. These things get forgotten too easily as well, especially when the fighter gets to choose a -1 penalty to Cha for a week.
You seem to be making two points here. If I've understood you clearly, first, you don't like additional penalties, and second, you find the game effects more forgettable.
As far as additional penalties, I can't say that I see a big difference between your suggested houserule and mine. You create a new score to track and impose a penalty on the number of healing surges. I let the player come up with an injury and penalize some (most likely) rarely used skills a little, removing the penalty with existing mechanics (Endurance, Healing, "Remove Affliction" ritual). I can't really draw a clear conclusion as to which houserule seems "heavier", but I do think mine will affect the game mechanic less frequently. I must admit, the concerns stated in your OP make your rule sound a bit "heavier" to me, but, again, I'm not sure. I certainly would have no real objection playing with your houserule.
With regard to the second one, I am not trying to gimp a character. I'm trying to make the narrative a bit more realistic and the game a bit more fun. By letting the player choose the wound, that goal is achieved, and the fact that the player has an active role in this mechanic makes it less likely to be forgotten, at least in my mind.
Keeping bonuses and penalties either permanent or short (one round/encounter) in duration seems to be a conscious design choice in 4e for a reason.
Setting aside what kind of duration is more fun, I agree, the reason you refer to being a conscious pursuit of simplicity (again, ignoring whether this is truly achieved). Personally, I find my houserule simpler, but we can both just impute that to confirmation bias. In terms of real in-game effects, my houserule will probably see less impact on the game mechanics (the most common effect will be a tiny penalty to some skills the character rarely uses), but the fact that the player gets to choose the penalty allows them to ham it up in roleplay, which is what I'm more interested in.