I haven't played the iOS version, but I have played the PSP and Wii versions of the game.
Somethings to note about the Wii version:
1) Visually it is perhaps the least impressive of the three main versions. It's FF6 sprites running around in FF4 environments, practically, which can be a bit awkward. At the same time there's a weird enhancement to the nostalgia because of the reused assets.
2) The game is the most exploitable version of it, in that, if you're fucking insane like I am, there are RNGs to guarantee you all of the ridiculous rare stuff like Rydia's summons and the tails and challenge dungeon stuff.
3) It's also the least well put together version, I'm willing to bet. I once got stuck in a battle because enemy AI had two snakes using constrict on me ad nauseum. Damage was being done at a minimum, meaning game over would take forever, and there was no chance of breaking free and attacking or running. Other glitches abound.
Of note regarding the iOS version is that it uses the same style as the DS version of FF4. Many people did not like that presentation, but I was pretty okay with it. Assuming it is mechanically more in line with the PSP version of the game, then:
1) Challenge Dungeon prizes are easier to get without doing a ridiculous RNG, but you can only get one of each, so no Challenge dungeon farming (why would you want to do that anyway?)
2) Rare drops are still rare, but with the difficulty adjusted from "Tokita is jerking off to your tears" to "Playable" you don't need them as much.
There are only two rare things I recommend players bother going for in The After Years, regardless of which version: first, the Mythril parts in Rydia's chapter, so that you can unlock Calca and Brina. They're not exactly great characters, but I'm the kind of person who loathes missing out on characters in a game. Second, the Black Tail in Palom's chapter. Unlike the other tails, there is a guaranteed, simple way of getting it regardless of version. Unfortunately, it requires an enormous amount of gil (literally more than the maximum amount of gil you can have in your inventory) to acquire both the Black Tail and the Queen's set in Palom's chapter, and in Palom's chapter the gil acquisition rate is barbarically low, meaning many people (who are all saner than I) will not feel the need to grind for cash to acquire both. As a bonus, though, grinding for cash in Palom's tale significantly increases your chance of getting the Wizard Summon. As a downside, you're likely to hit the level cap for the chapter well before you have the money you need.