Then you should not be able to advance the skill further without the perks. Otherwise the skill and level readings are just a lie. Either you have a skill of 90 or of 95 or of 100, or you don't. If you do not, certain perks won't be available, however if you DO, then certain abilities should be available without the perks. Perhaps not extremely potent benefits like 50% off master level spells, etc, but novice level spells should all already be at extremely reduced magicka cost once you have reached a mastery skill level.
The skill rank provides some concrete benefits in and of itself but exists primarily as a measure of your experience in the skill. The perks themselves are the true measure of your ability, which is why I and many others have been saying all along that they should have gone with a different name. Todd Howard stated this in multiple interviews. The specifics of what the skill rank does for spells have not been revealed but I've heard it rumored that it increases the spell's potency, e.g. even unperked your basic Flames spell will do significantly more damage at skill rank 100 than it would at skill rank 15. If they don't do that then I'm sure they'll go the other route (which I disagree with), namely reducing the spell's casting cost.
What I like about the new system is that it makes you choose. You can no longer be good at everything, thus you have to carefully consider what you want to do and who you want to be. Every advantage you've gained is one that you had to work for and that had to come at the expense of not choosing another strength. I know you liked the old system because it gave you the choice of being good at everything. The fact that that "choice" existed in prior games always bothered me, because it trivialized the whole experience of leveling up. I never felt like I'd had to work to get to where my guy was. Quite the opposite, I felt like once I passed level 20 there was no challenge left in the game, because there was nothing stopping me or even hindering my progress in becoming a do-everything god and I quickly became bored with it. Being super-powerful is great, but being ALL-powerful is just boring to me, and I've always hated the notion that there's nothing wrong with a game that forces you to make your own challenge, because that's something the game should do on its own.