I think that's kind of the point of being high level? At least against mundane opponents. I, personally, don't find it a lot of fun when about 98% of the NPCs are only much use during the day (shops, blacksmiths etc) when, surprise surprise, being a vampire isn't so good. It's not 'challenging' to have to keep necking health potions in town because you have a ton of stuff you need to sell and you can only do so during the day, that's annoying. Borderline frustrating. Also, there's no incentive to get to higher stages of vampirism if doing so means you turn into something like a barbequed skeever-burger within a few seconds. Again, no challenge, just annoyance. Having to balance the stat penalties and fire weakness during the day is more challenging than unavoidable damage.
Also, 'becoming immune to nearly all magic' is not unique to vampires; my Nord warrior is pretty much immune to all magic because he's wearing half a dead dragon that's been enchanted to Oblivion and back. So is my Breton mage, because she's a Breton, coupled with alteration perks and a few items.
I was saying there's no need to diminish the weaknesses if you're going to be practically invincible at high levels anyway, not that you shouldn't be strong at high levels. You should. But if your so strong at high levels (and considering very few characters use fire magic OR silver weapons), diminishing these weaknesses is kind of pointless since they really aren't going to be having that big of an impact on you in the first place.
Also, if you didn't like being attacked at Stage 4, you should feed regularly. I know that makes you weaker, which is in and of itself, a whole other stupid decision, but them's the breaks.
As for being immune to magic, while it's true that all people can become nearly immune to all magic, vampires can become COMPLETELY, as in 100% guaranteed magic absorption, which makes that weakness totally moot. That IS a unique feature to vampires. With the right perks and stone in place, you won't ever have to worry about ever getting hit with a spell. Necromage + Atronach Perk + Atronach Stone = Total Magic Absorption.
As for having to sell things during the day, I agree. There should be some shops only open at night. Gives the cities more life to them, which is always a good thing.