I've done builds of nearly all of the characters in the DC Handbook, and a fair few more besides. I've done fewer Marvel builds as I read a lot more DC.
I've upped the stats and PL of a few characters when doing my own builds.
I've pumped up Aquaman to PL14, making him a lot stronger. When wielding the Trident of Poseidon he is PL16, as that is supposed to be an artifact of immense power.
My Atrocitus is PL15. He is supposed to be a terror of the cosmos from all I have seen. Related to this my default, run-of-the-mill Green Lantern is PL14. Each is supposed to be a mighty champion of good and justice after all, capable of protecting an entire space sector.
My Big Barda is PL14. I've upped her to JLA levels as she is the former leader of the Female Furies and in the books she is very often referred to as one of the mightiest warriors around.
Likewise I've upped the power levels of Power Girl and Supergirl by 1 PL each. With Power Girl it's a bit of fandom, as she is my favourite character. With Supergirl I've brought her stats more into line with those of other Kryptonians, with whom she has always shown she can hang.
I've jiggered Lady Shiva's stats such that without her Body Reading power she is 'only' PL12. Still an incredible fighter but to reach the level she has she does rely on a super ability.
My Talia is PL10 and now a master martial artist and assassin, capable of taking on notable heroes.
I've elaborated Metallo. He is PL15 against Kryptonians, but effectively drops to PL12 against everyone else due to Limit (only Kryptonians) on some of his powers.
I've upped Starfire to PL13, greatly increasing her Strength and Blast power. She is now much closer to a Kryptonian in power.
I've increased Jade a bit to PL12, bringing her a bit closer to her father. I'm not sure whether I should up her to PL13. Maybe.
I've also made some systematic alterations to the stats given out. I've reduced the Strength and Stamina scores of many characters according to the following schema:
0 Ordinary man, fit woman
1 Fit man, strong woman
2 Strong man, very strong woman
3 Very strong man, peak woman
4 Peak man (no ordinary woman can reach this level)
Stamina as above, but women are not held to a value 1 below that of men.
As a convention in my builds I've limited how much Fortitude defence can be raised. No character can have more than 4 points allocated to it. I don't allow characters to be that resilient over their Stamina score. This has also had the advantage that I've been able to bump some characters Will defence up. My Batman now has a Will defence of 16.
I've also sought to harmonise builds, making them more mutually consistent in how they depict characters. One way in particular is to carefully distinguish between powers and ability scores. My Superman has his massive Strength score as a power, rather than as an ability. I've also altered his defence scores. My Superman has a Fort defence of 18, but only a Will of 12. He does get mind controlled a fair bit.