I can think of a few reasons for this change.
1. Game balance - forcing mages to level lockpicking prevents an all-out focus on magic that helps control how powerful the mage becomes.
2. Reduce powerleveling. I've heard (not a mage) that spells only level when they are actually useful. So for example, spamming stoneflesh has no benefit if there aren't enemies around. This restriction would be difficult to program for waterwalking and would be meaningless for unlock (just run around town at night and cast it on every door).
3. Allocation of developer time. Of course, this would only apply to waterwalking, not the unlock spell, since the tower stone already does that.
Illusion has a spell called "Clairvoyance". As far as I can tell, Clairvoyance doesn't cause any progression of the Illusion skill at all. So, why not a few other spells that provide no progression, but are still useful?
I don't understand why other people feel like things have to be taken away from other players who want them, in order for the people who *don't* want it to be happy? Don't want to use an unlock spell? Don't use it. Why should it be removed from the game? It's a single player game - you don't need balance. The player can choose to become as powerful as they want, don't see how that hurts anyone else? They can choose to stay relatively weak and keep the game challenging, they can choose to use the lockpick skill and be a thief, or use the unlock skill as a mage, that's their choice. That's what I loved about previous Elder Scrolls games, and while I overall like Skyrim, I'm finding myself very disappointed with the design of the character system.
If anything it seems to be regress (for those of you not familiar with that word, the opposite of progress is not congress [as the old joke goes], it's regress - to go backwards). Not that the old system was perfect - I hated the fact that in order to not end up with really screwy stats, I had to artificially level things in an awkward fashion (e.g. levelling up endurance skills early, because of the fact that health gain from endurance is cumulative from level 1, instead of being able to level up endurance later, or gradually). But, I really like the idea of spellmaking to allow you to "level up" your magic over time, I like stat enhancing potions, enchantments and spells, I liked having 60 different spell effects (well, maybe not quite literally 60, but having a large diversity of magic).