I think it's mainly just that we're so used to seeing such stat/parameter differences playing out through progression, rather than being a permanent thing maintained throughout the character's life,
If you're comparing it to D&D, this is a similar progression except for two differences: 1) we maintain differences between classes (given equal level) as an integer rather than as a proportion and 2) because we use a 100 point base scale instead of a 20 point base scale, we have finer control over per-level advancement.
E.g. in Pathfinder, a fighter starts with +2 Fort, +0 Ref, +0 Will. They progress like this (Fort/Ref/Will)
5th +4 +1 +1
10th +7 +3 +3
15th +9 +5 +5
20th +12 +6 +6
A rogue starts with +0 Fort, +2 Ref, +0 Will. They progress like this (Fort/Ref/Will)
5th +1 +4 +1
10th +3 +7 +3
15th +5 +9 +5
20th +6 +12 +6
It's a regular progression: they start with an advantage in one (for some classes in D&D, two), and advance at regular intervals. Of course, at high levels this falls apart because the proportional gulf between good and bad saves becomes so wide that characters have to overcompensate or inure themselves to specific effects to avoid being sucker punched. At 1st level, the difference between the good and bad saves is (effectively) 10%. At 10th level, it's 20%. At 20th level, it's 30%.
To make matters worse, typically the obvious "good" stats for a given class reinforce the better saves and neglect the worse saves. Fighters often have a high Con, which means they are likely to have an even higher total Fort than normal. They might have a decent Dex which can bolster their Reflex, but it's rare that they have a high Wis (and consequently, Will save). Because save DCs are often balanced around the "hard" targets, it means that the weakest saves of a class combined with the weakest (or least important) ability scores for that class make them really, really vulnerable. This is why Pathfinder has a special Bravery feature for fighters at higher levels -- otherwise they'd run or freeze in terror more than half the time a comparable caster chucked a Will-based fear effect their way.
In PE, fighters start with the following defenses: 25 Deflect, 15 Fortitude, 10 Reflexes, 10 Psyche. Rogues start with the following defenses: 15 Deflect, 10 Fortitude, 30 Reflexes, 5 Psyche. Every level, every character gains +3 to all defenses. At 6th level, the fighter would have 40 Deflect, 30 Fortitude, 25 Reflexes, 25 Psyche. The rogue would have 30 Deflect, 25 Fortitude, 45 Reflexes, 20 Psyche. The fighter's worst defenses are still Reflexes and Psyche, but they're only "just as" bad (by the same margin) as they were at 1st level. The same applies to the rogue's Psyche and Fortitude. And while the rogue did "catch up" to where the fighter's Deflection was, the fighter maintains the same 10 point advantage over the rogue that he or she did at 1st level.
Of course, Attributes, gear, Talents, Abilities, etc. also can all feed into your defenses, but those are much easier to switch around than your class and level. I.e., if you find yourself particularly vulnerable to a particular type of attack (meaning, what defense it targets), the cause is likely easier to remedy in PE than it would be in D&D (because class is such a large component of that value as levels rise).