Untrue. Every skill in Oblivion had four perks, and each of those perks had some significant impact on the game, which is quite a bit better than Morrowind's approach with the skills. The issues there were more with how the skills were used by the actual gameplay systems (overly aggressive leveling, simplistic combat, and a few simple exploits made a lot of them more or less irrelevant), but the skills themselves were considerably better-developed and more complex as a result, and in some cases (archery) losing the other skills allowed them to make pretty clear improvements to the system that the remaining skill used.
We didn't "effectively get less". We effectively got something different. You didn't like that something, but that absolutely doesn't mean that it's something less.
Perks were only experienced as time went on. I don't see these perks as adding any depth at all. How is having a few fancy additional combat moves adding depth to the game? How was the rotate thing for speechcraft adding any RPG depth? It wasn't. The speechcraft thing obviously not, and the combat moves are action game features more than anything else. I didn't even used those combat perks. Yes, the point of an RPG is to be able to ignore things, but not make the experience less "deep" (that's convincing yourself that it makes the game deeper).
Okay, this can't keep going, it's getting ridiculous. Please, please EXPLAIN how you would make a character build that relies on the character being able to run fast but not jump high as a major element of his character in this series. Please. Don't give a vague response. Don't give a response implying that it's because you're losing skills, or say something like "because it is". Don't talk about it in terms of how it's going to impact game design, because we're talking about character builds in terms of roleplaying here. Now... explain.
Who told you this had to be a major element? It doesn't have to be major to be important.