Problem: Powerful souls=summoning
Solution: make summoned souls unable to be soultrapped
Problem: stones=azura's star (it was in morrowind and oblivion it's probably going to be in skyrim or something similar),
Solution: change the abilities of azura's star
In TES, summoned creatures can be soultrapped. Also, Azura's Star is a daedric artifact. Its abilities are already set. It's bad enough that BGS likes to bend TES over with each new installment, but if they're going to start changing the lore to cover up their bad ideas and laziness, that's just going to piss off even more people. Having Enchant as a skill is just gimping it. It should stick to the altars and cost money so that powerful enchantments cost LOTS of money as it was in Morrowind. That way it's balanced without limiting your enchantments and making enchantments weak and restricted. Also, that would allow scrolls to be made without the problems already discussed because a powerful scroll would cost amounts of money that would take a long time to accumulate.
Daggerfall is probably one of the most non-linear story driven game out there. Morrowind was a little more linear, a little more restricted, and that's not good, but fortunately it was still an amazing game. Oblivion was a LOT more restricted and it felt shallow and robotic, and you were given a LOT less freedom (locked doors that require keys, skills with a cap-off at 100, where even skill fortifications had no effect upon raising a skill above 100, loss of a lot of cool spells, a gimped magic and enchanting system, less armor slots, etc...). It was more balanced, but balance should not be achieved at the cost of fun, at the cost of gameplay, and at the cost of many of the things that make the game what it has been. Balance should also not be restrictive. If something is easy to exploit, the answer isn't to remove it but to make it a challenge to achieve.
As I said before, if making a scroll that does a bajillion damage is overpowering, then make it cost so much money that you'd have to play dozens of hours to accumulate it, that it would be a focus and that you would have to go through a lot of the conventional, standard gameplay to get there. That way we can still have overpowered enchantments and spells, but we have them as a reward for a lot of effort and time and thought to get there.
Under that philosophy, all the people who completely lack self discipline (I'm looking at you people who say "I want the game to be balanced, and I hate stuff that's overpowered because then I use them when things get difficult. I'd rather not use them and I'd rather do things in a way that's more challenging", which is perhaps one of the stupidest things I've ever heard) would be less tempted to go for the same things a lot of us enjoy, not to mention achieving the level where you can make your character that powerful would put you through a lot of that gameplay those people prefer anyway.
But this is only me speaking in ideals. gamesas is obviously going to continue to limit and restrict and gimp every new game they make until eventually TES games will be developed by Square-Enix and BGS will just publish them.