I think it's a matter of 1)Square hasn't ever put out a good F2P mobile game, 2)Square sticking iaps and time limits onto the game is not a good sign that there will be any depth to it at all, and 3)people are not exactly inspired to have confidence in a company like Square Enix anymore.
I think Guardian Cross is a pretty good free to play game, I enjoyed my time with it. Sure, it has micro transactions to replenish your energy and all that, but they're completely optional. Granted, I never "finished" it i.e. I didn't see the storyline to completion, but I got pretty far before the 2.0 update hit and it was pretty well balanced, which is why I don't think this game will be a cash-in.
I think there's a huge problem re: mobile games, where a lot of people tend to associate free to play with something like mobage/GREE games which aren't really... games, I think, but there's also the free to play games that actually have gaming to be done in them, like Kingdom Conquest, Puzzle and Dragons, Guardian Cross, Sengoku Rumble, Real Racing 3 and many others. SE has already released a lot of free to play games for the mobage/GREE/mixi/Facebook/whatever else platforms which are basically all money grabs, but they've released just a few "real" free to play mobile games, all of which, in my opinion, are of high quality with balanced gameplay mechanics that don't force you to make microtransactions to win, and I have the feeling Agito will be like that, and not a mobage/GREE-type game.
For that reason I think it's silly to assume that just because a game is free to play and has microtransactions automatically means it's gonna be terrible, whether it's made by SE, EA, Capcom, or whatever. There's a lot of great free to play games both on mobile and other platforms.
Consider: Square puts two Final Fantasy games on the iOS etc platforms. One is full of depth, contains a chapter-based, job-class filled, full-length RPG adventure with no iaps, no time limitations, and no other mobage/social hijinks. It is in every way considerable a classic-style Final Fantasy game. The other is a mobage game with no music, iaps, time-limit/energy limitations, full of advertisements like a piece of freeware, and can be played with one hand while taking a dump for all the player input and thought it requires to get through it. Literally tapping one button will get you through basically the entire game until your time points run out.
The first game is Final Fantasy Dimensions, and it costs 20 dollars American to play, which is a ridiculous price for a game on Android or iPhone or whatever else. The other is Final Fantasy Airborne Brigade, and costs you only what they can swindle out of you by misdirecting your thumb toward the cash button.
Call me cynical, but would a company like Square Enix, which charges an arm and a leg for an SNES level experience, really just give away for free a game that is on par with something they were selling on the PSP for 60ish bucks?
I cannot honestly fathom a world in which Square offers any manner of "deep" gameplay experience for free or even "free". Heck, if I was running the company I sure wouldn't. It would be a colossal waste of money to expect people's iaps to pay off a game like Type-0.
Regarding the pricing on paid mobile games SE puts out, I think... they're fine. It's true their games are generally more expensive than the dollar many users seem to be used to paying, but their quality is also a lot higher. I have no problems paying for quality if that means getting games like Chaos Rings II or Drakerider which would have cost something like $40 on 3DS/Vita/PSP available for a half of that or less on launch day.
And even then and despite how SE's paid iOS/Android games have been hugely successful for them, they've been lowering their prices even more lately, with things like Bloodmasque costing like $7 at launch and like $3 on sale. And now they're selling even more.
