Well, let's see...
1). It was in a cycle with cards with much higher apparent power. Whenever we get cycles, we're not especially used to most of them being good--I imagine if that you looked at cycles over the history of the game, you'd see pretty consistently that 1-3 of the cards in a 5-card cycle will see play--the Commands, for example, have Cryptic Command, which is amazing, into probably Austere Command, which is clunky but functional, all the way down to the mess that is the red command. So when we're presented with a cycle, we're conditioned to assume that at least two of them aren't good. Gideon got to be a 2/1 for 1 with upside even before he flips, which is very powerful looking (even if Kytheon's made no appearances), Nissa got to have the walker side with the 'biggest' effects--draw a card, make a 4/4, and a strong ult. Liliana had her zombie, although she wasn't as impressive to most as Nissa or Gideon. Jace was hard to evaluate, so people assumed that he would naturally just slot in to the bottom of the cycle and keep Chandra company.
2) Planeswalkers have been finishers lately. Ugin and Elspeth are both strong control finishers that quicly take over a board state. It'd been a while since Stormbreath Sarkhan had really seen play, but he filled a similar curve-topping niche. Xenagos was a value factory, but spitting out 2/2s is very different from what Jace does in terms of how it puts you ahead in the game. Ashiok was a control finisher. Really, it's not until you go back to Jace, Architect of Thought that you really have an incremental value planeswalker, and even that is mroe of a finisher that Vryn's Prodigy. We were evaluating him with the wrong set of tools, and we had been burned on Narset not too long ago.
3). We had forgotten how strong Merfolk Looter was. It's been a long time since we've been able to play with Actual Merfolk Looter. We've had a lot of three-mana looters in limited, and a lot of looters that you have to pay mana for, and they have all turned out pretty bad. So that's the context that most people were familiar with looting in. While I do think that Merfolk Looter itself, with no additional upside, would be questionable today, Jace does bring that upside (except this, too, got horribly misevaluated). Plus, if you discount the walker side, as so many people did, it even compares unfavorably to Merfolk Looter, if only slightly--it can't attack, and eventually you stop being able to loot with this. There were a lot of people saying that they'd rather just have the looter than have the flipped Jace.
4) His +1 reads very poorly. It's been beaten into our heads that a planeswalker has to protect itself. Shrinking a single creature slightly looks like a miserable attempt at that. It's not Vraska-tier nothingness, but it still looks like you're basically doing nothing when you plus him. The truth is that shrinking a creature is actually really strong when it's free (just like how much stronger looting is when you aren't spending mana on it). It's not precisely the same, but I've been getting late Dampening Pulses in BFZ draft, Creatures are very carefully priced, stat-wise, and taking even a single point of power off a creature makes it look a lot worse than you'd expect. What would we think of Siege Rhino if it was always a 3/5? What about 2/5 Wingmate Rocs? 2/3 Mantis Rider? -2/-0 goes a lot further than we expected.
5) His -3's easiest comparison is to Snapcaster Mage . Snapcaster is probably the best blue creature ever printed (although Jace is up there too now). We'd become accustomed to seeing Snapcaster in action, and particularly seeing the plays made with it at instant speed. Snapcaster, block your guy, bolt your other guy. Snapcaster Mana Leak. Snapcaster Cryptic Command, if you're feeling really saucy. Compared to that, you've got an ability that you have to pay a big - on, and you'll only be able to activate it on your turn. That is, indeed, worse than Snapcaster, who also comes with a 2/1. The tradeoff, of course, is that Snapcaster costs you two mana before you flashback the spell, whereas Jace costs you none. Like looting, this is an effect that is much stronger when it's free, and we estimated the tradeoff poorly.
6) His Ult is Bad. Now, people do say to evaluate Walkers without looking at the ultimate, but we can't help but look--especially when we're in the mindset of using it as a control finisher. Now, Jace's ult actually is pretty poor by ult standards--it'll win you the game, but it takes you a lot of turns of 'only' shrinking creatures to get there, and even then it's pretty slow to actually deliver the win. Because the ult looks so bad, it led us to try and find a play pattern that maximized his one useful-looking ability, his -. People imagined a pattern of -3, +1, -3 being the most typical (because shrinking is worthless, right?), and the last planeswalker with that particular pattern was Vraska, who is hot garbage, and Jace got tainted by the mental association.
7) We didn't understand what flipping a planeswalker implied for gameplay. Part of the reason Planeswalkers defending themselves is so critical is because you're frequently tapping out for them. But when Jace actually becomes vulnerable to attacks, you have all of your mana untapped on your turn, and you're completely free to set up the defenses for him, and it's easy for his contribution to push that over the edge. So that's another way we just had the wrong context.
8) Ojutai's Command wasn't really on the radar. Other frequent Jace flashback targets, like Dig Through Time had seen play (but were I think a little out of favor in the face of ABZAN), but we didn't understand what kind of toolbox in one card his -3 would give you access to. We especially didn't consider how with Jace it has the secret mode of "Get Back Your Planeswalker From The Graveyard". It gives Jace an added level of resilience that we just didn't expect. It lets you trade him for their removal and be fine with it, because hey you'll just have him back in a couple turns.
There's probably more than this, but I am tired now. Enjoy the words.