Splitting your post up into smaller quotes because I responded point by point - not trying to misrepresent your argument or anything like that.
Am I going to have to get a perk to be more balanced?
I don't imagine there'll be balance perks, particularly, though maybe under armor (more agile use of armor = harder to knock over because you're more in control of your momentum). Perhaps pick up a perk for blocking or parrying to allow you to stop those knock-down blows before they hit you? Why satisfy yourself with just one way to go about doing something when you could approach the problem from multiple angles?
Am I going to have to get a perk to jump higher?
The removal of Acrobatics means I'd say probably not, but the gameworld probably isn't going to be made to keep things from people who can't bound over buildings like Superman - the ability to jump probably simply wouldn't be that relevant of a skill. And if there WAS a perk to increase jump height, I don't see anything much wrong it - though I have no idea how they'd fit it under any of the current skills.
Am I going to have to perk up in order to be rewarded for using the skills of being a real life person interacting with the world?
Well... why not? You learn by doing as much as you learn by studying, don't you? Frankly, I've only recently started to learn to cook and was just learning how to boil rice a couple months ago. It used to take me hours to chop vegetables for a dish - I was incapable of making supper in a timely manner at all. Now, I'm still slow, but I've cut prep time for most things down to an hour at most through the use of new techniques I've naturally picked up just from using the knife. If the overall skill is Cooking and I've been working on it for a while, I'd consider that taking a perk in knife handling.
Am I going to have to get out my trusty spreadsheets in order to determine what magic perks can be done away with to ensure that my mage that has been running back and forth from one side of the country to the other battling dragons has some semblance of strength or is he going to be as weak and unbalanced as some bookworm that's never left the library?
I think you're overthinking things - spreadsheeting probably only matters in particular when you're optimizing a character, and that is certainly fun to some people but you seem to want more immersion and RP. To that end, why bother worrying about how many perks you can "spare" to get a character that fits your concept? Make choices as you're given them and build your character organically, then deal with the challenges that arise from inefficiencies in that arrangement (or, perhaps, enjoy the benefits of unexpected synergy). Isn't that the point of roleplaying? If Beth manages to balance the game well enough, it shouldn't be possible to gimp your character into unplayability merely by taking a few perks for flavor instead of optimization.
Will my mage (with no intelligence or will power attribute) be able to dangerously chug fortifiy willpower/intelligence potions, taking their conciousness beyond the scope of the normal reality where the only the uber high power potions/incantations/spells can be done?
Or will all of this be lamely confined in a magicka meter and skill perk? (perk: press B for Awesome spell!)
You could just represent that a different way and get the same effect - chug Fortify Magicka and Fortify (Skill) potions. Once you're sitting at Destruction 150 and have a pool of Magicka as deep as the sea, I'd say you're capable of performing feats of magic far in excess of anything a mere regular mage is capable of. You're on a different plane of existence - the only difference is what you're buffing, not what you can do with it. It means you have to use more focused buffing items, yes, but that's a relatively minor thing - I mean, if you're a skilled enough alchemist you should have no trouble churning out skill and magicka-fortifying concoctions. Hell, after all that time spent focusing on the craft, you might even pick up a perk or two towards it to help your output. The sky's the limit.
EDIT: Updated my post to reflect changes in yours.