"Nuckles" and the Pender's characters. How would have you written the Echidna?
Damn, can't really get away from this one forever can't I? Well it's not like I hate the background of The Echidnas in Archie Sonic, I like it I really do but god damn is it complicated! I'd make it much more smoother, a lot less convoluted, and give it a lot of wiggle room so that stuff like Sonic Adventure 1's Story Arc can easily be intergraded into the mythos.
For one while the Brotherhood members are still relatives I think if most of them are like cousins, uncles, distant relatives it would make much more sense. Why do I say this? Because a few of their members must be pushing 70 -100 by now! The oldest member when he was still alive was Tobor, TOBOR, I mean the guy looked older then other characters but damn man Athair looked older then him and he was his great-something grandson! Have you guys really looked at Knuckles family tree lately? Now you maybe be saying "But did the Hyper Zone make their ages screwy or something?", Or something as that's not the case. From what I remember they can live for a long time do to exposure from the Emeralds for so long. Now I CAN buy an extended lifespan due to the Emeralds but that's really pushing it when it comes to them. The only way I can think of how it makes sense in the comic is that the guys in Knuckles family are really smooth and moves fast when young. The Family Tree here is a straight line when you look at if, if it was more branched out maybe it would be better and there would be a lot less confusion.
The Dark Legion I have no real problems with, granted the family tree there is (thankfully) MUCH shorter then Knux is but you could count that as due to time moving (and actually confirmed to be) screwy and slower in the Twilight Cage. Yeah I got no problems with it there, I do wonder why all the women Echidna have there names like Jani-Ca or something-lu but maybe you guys know about that. As for The Nocturnus since they have yet to appear in the main storyline I'm sure they will be fine, I know the Archie Sonic Team WON'T make the same mistake Penders did by over complicating it. Though it does make you wonder why the Dark Legion and Nocturnus never did anything together...then again both sides have their own goals.
How would I work the Knuckles Clan in? I'd probably either have them where they are now in the timeline OR have them during the time before the Brotherhood and Legion. You know so that after Perfect Chaos is sealed some Albion Echidnas go to discover the Knuckles Clan Ruins and find the Emeralds, thus kick starting everything from there on out, from Enerjak to the Brotherhood.
I think I just made things much more simpler with those concepts alone, say what you will about the "Reboot" but the Ian and Co. can REALLY fix things up when it comes to the background of the Echidna Race, and to be honest it's been LONG overdue. Penders had some good ideas, I'll give the man credit, but he didn't exactly plan EVERYTHING in the backstory, neither did he give it some wiggle room should future Sonic Games dive into Knuckles' Backstory. So naturally things didn't pan out so well in the end and later Knuckles Plots due to the Comic's Cancellation were cut much shorter then he originally planned. If I could give comic writers one hint of advice it would be this, PLAN EVERYTHING, especially backup plans for backup plans! But for it's time it was really interesting and I'll say this, Penders' concepts for the Echidnas is pretty out there when looking at the genesis games but it worked at the time and shaped how a lot of us view the Echidnas as we do now. The biggest influence I'd say the Archie Comic had with this background was the game Sonic Chronicles, what other games will take influence from the comic as well is uncertain, but it's an interesting though.
Seriously, HOW THE HELL did nobody know that Robotnik was evil!? I mean just look at those red, glowing, hellish eyes, oh yeah I can completely trust that guy with my life! *sarcasm*