First, because you can assign flaws and extras
Flaws reduce the cost of the power, and thus allow for a more efficient use of power points. For example, if I was making a character like Iron Man, I could give him a whole slew of Enhanced Trait powers representing the general superiority of wearing a suit like that, but then give them Removable 1 (among other things) to represent that the suit can be removed and the powers lost. Its used as a power and not as equipment in order to represent how core it is to the character. Iron Man's suit is a power, a kevlar vest is equipment. Limited is also a good power, Superman would likely have a whole slew of Enhanced Traits, but with Limited (Kryptonite) in there somewhere. And note, the Limited flaw has a fairly dramatic effect on the power cost.
Admittedly it doesn't look like there are that many extras that might work well. But the same concept applies, of allowing you to add interesting flair to the Enhanced Trait. Indestructible could at least mitigate a Removable trait, Innate prevents your concern with nullification. Subtle has interesting effects as well as it could cause a character that appears weak to be in fact be unnaturally strong, that sort of thing.
Obviously, it takes a good GM to properly handle the flaws on powers to prevent them from getting out of hand ("No, you cannot take Limited 1 (power does not work in space) for a game that will only take place in Seattle"), but results in fairly rewarding games if you can put interesting flaws in there.
Second, it allows it to be used as an Alternate Effect
This means you could have a sort of "dial" of powers that you can switch between while having an overall reduced cost than having each of them individually. You just have to accept you can't be both super strong and super agile at the same time. But you could say have something like Funnels from Gundam, that can defend you by deflecting incoming attacks (Enhanced Trait Dodge), but then can also be used as an attack. The trade-off is it can't attack and defend on the same turn.
Third, it allows for the use of descriptors with your powers
Your agility might be tied to water, and that might have very real affects on how your power interacts against someone who's power is say, based on fire. See M&M3e p.154 for more on that, its a whole part of the system.
Fourth, you can use Extra Effort to increase the magnitude of the power
(Thanks to @Sean Duggan for pointing this out) Per p. 19 of M&M3e, you can use Extra Effort to increase the rank of a non-permenant power by one, until the start of the next round. This also bypasses normal PL limits, so in theory you could use Extra Effort to increase an Enhanced Trait Fighting. That would improve your Parry as well as Melee Attack accuracy.
Fifth, your GM may impose limitations on buying abilities and other traits
For example (p.55 M&M3e), 7 is often considered the "peak of human achievement," and some GMs may require that a human character in a M&M game at most only have 7 in an ability (and thus anything beyond that is a power).