How come half of the champs in this game now have only a single "choice"? Especially at rank 2, what's the point of levelling a guy up? This kind of defeats the purpose of the leveling system...and it seems to be happening more and more....why??? I think the new set is really cool, but I hate most of the changes to older runes
The champs with fewer upgrade choices are the exception, not the rule. There should really only be a handful of these. They are also typically limited to C and UC champions. The specific reason they exist is because there are cases where adding additional upgrade choices diverges too much from the intended role of the champion. I do think these should be avoided where possible, and I may go in and try and add some upgrades to some champions down the line that currently have limited options.
Incidentally, if there are examples of champs like this and you have a good idea for an addition, feel free to message me or post in the Cactuar Crate.