Frankly, the only difference I see is that in one system, it is a (derided) "house rule" and in the other system, it is a ("groundbreaking") "module".
I can see where you are coming from. Personally, I just took the "different systems in different classes" design as an opportunity to tinker and shape the system to my preference. Essentially, as a selection of modules for me to choose from. My group likes the Sorcerer casting system better than Vancian? Okay, all "Wizards" in my game use the Sorcerer mechanics, and there is no Vancian. But then, I'm a tinkerer. I see the Hit Dice mechanic, and even though the rules don't explicitly
say, "You can roll Hit Dice randomly, or you can set the recovered hit points to 'full', 'half', or 'quarter', or even use 4e Healing Surges as is," that's exactly what I
see.
But, as I've lamented somewhat in other threads, that's not the paradigm these days. I think a significant plurality, if not a majority, of D&D consumers now want such options clearly spelled out. Mearls & Co. originally intended to make magic system part of the player's customization options -- choose Class A for Magic System B. But many folks wanted this customization to be on the campaign side.
In the WotC design paradigm, which favors greater integration than the TSR one, there is a distinct difference from a design perspective. The way the options are integrated and balanced is different. Siloing the powers in different classes creates different flavor for each one. For some, this is a tenable work-around. For others, particularly for folks who want a concrete set of rules to work with, it is not so workable. It creates cognitive dissonance if they refer to "wizards" at their table, but must use "sorcerer" to interact with anyone outside that group.
I think it very much behooves the design team to pay attention to issues of presentation in this way. If the guts of the system are not really that different (as you say, although I may not entirely agree), but the presentation makes it amenable to a larger audience, that's a win-win. We're dealing with people. "You're looking at it the wrong way," valid though it may be as a point of view, is simply not good marketing or presentation. As Twain said, "In matters of opinion, our adversaries are insane."