My opinions on the Crystal Scar aura, that I have been going over with a game designer friend:
The penetrations are probably a little high. It should have to be a conscious choice to itemize into doing true damage to enemies, even through their defenses, but I see brutalizer/lw and haunting guise/sorcboots/abyssal scepter becoming core build items on everyone. A possible fix would be to reduce the percent values.
Armor pen and Magic pen have separate problems, which are due to the value of using runes to spec into flat pen (25 for armor, 15 for mr, marks and quints) and the itemizability of the stats. There are only a few choices for armor pen, so ghostblade/last whisper is seen very frequently, and sometimes is rushed. There are similarly few choices in flat magic pen, and only one choice in percent magic pen. Mages tend to have high base damages that scale better in the early to mid game with penetration than they do with AP, which means rushing haunting guise/sorc boots is usually the best option.
The mana regeneration does not appear to be benefiting anyone that I can identify. Spammy champions or those with high mana costs still run out of mana, while low mana cost bruisers and fighters don't. Building mana regeneration always feels like it is less useful than building max mana, as there are plenty of excellent choices for building max mana (sheen, frozen heart, catalyst and upgrades) no matter what class or champion you are playing. Problematic use of mana seems to come from champions that only have to lightly itemize into mana to be essentially 'manaless', typically fighters who build sheen or triforce. I think that a better solution would be to have the global aura increase regeneration significantly, but reduce maximum mana so that it's not trivial to itemize into infinite mana.
One thing I would like to see in the crystal scar aura is an interaction between the Crystal Scar and alternative resource champions. Champions utilizing Rage or Energy typically have a hard time, due to difficulty building up full Rage, or by using Energy on burst too fast.
I think that class specific bonuses sounds dangerous to implement, because it discourages alternative builds, some of which are stronger/more popular than the 'cannonical' bulid (look at AD Malzahar). However, percentage increases on bonus stats might accomplish the same thing, while still being technically 'flat'. If you provide a percentage bonus on bonus AS, AP, AD, etc from items, then only the champions that wanted to build those stats would take advantage of the bonus, but would still leave all champions to take advantage of it in principle.