I haven't quite given a proper response, largely due to the fact, that unlike some of the partisan marks, I actually think this was a close match-up in terms of how their reigns were AND in terms of their talents. As far as Champions go, Cena has been the Champ for about 6 years now, and for the most part, he still delivers every year, you either get a good year(2005,2006,2008 etc.) or a really outstanding year(2007,2009,2010). Austin was realistically only on top in the WWE for 3 years(1998-2001), so already, Cena has doubled his time at the top. Apparently some reports have stated that Cena's merch sales are quite close to Austins.
As far as ratings go, to say that "Cena pulls in 3's", and "Austin pulls in 6's" is incredibly ignorant. While Austin was definitely extremely over and the top guy, he was hardly the guy to give credit(single-handedly) for the ratings. If anything, what really got the Austin character over was not only the booking but the Vince McMahon character. Furthermore, you can't ignore certain factors, the wrestling/cable boom -- which meant that there wasn't a lot of competition since it was still a new thing(weekly Wrestling on national television). Today, there are like 200 more channels than there were in 1998, no matter what happens, what Vince & Co do, wrestling will NEVER be as popular as it was in the 90's(certainly not in the foreseeable future). So drop the whole "ZOMG Austin saved us" -- that is foolishly simplistic.
As far as the Austin character goes, in wrestling, it wasn't exactly too revolutionary. Guys were doing that sort of stuff in the territories(guys like Dick Murdoch), on a semi national level YEARS before Austin stepped into the WWE. So Austin most definitely did not revolutionize the business in that respect -- he merely emulated what was already happening on the territory level a few years ago and brought it to national television. To say that Austin was revolutionary(as far as the character goes) is to say that Shawn Michaels invented the Ladder match -- in the WWE fan's mind that might be true because they have been so hyped up by the WWE PR machine and haven't really seen wrestling before the 90's, but it simply isn't true. It is ludicrous. The ladder match was strong in the territories (including Bret Hart's territory, and it was Hart who brought it to the WWE afterall) long before Michaels did in the 90's.
As far as the whole argument with regards to "Cena would never fit into any other Era", it is BUNK. Cena has already proven with his gimmicks in the WWE(rapper vs now) that he has the ability to appeal to different sectors of the fan base. I would rather say he would have made a nice Corporate Champion back in the 90's. The idea that Austin was somehow timeless is also bunk. Austin's gimmick ONLY got over because people were tired with the early 90's and late 80's cartoony WWE -- if that hadn't happened Austin would not have been over. In short, time, circumstances, situations DO matter. Similarly, in a post-Attitude Era world, the Austin gimmick wouldn't work and that much is evident. Austin has made numerous returns(guest referee) and for the most part the ratings/buyrates that the WWE hopes for don't usually pan out. The Austin well is *dry*. Sure one last match would pay big but if he was a regular the nostalgia would wear out. No gimmick is timeless, everything is a product of its time. People seem to forget that a lot of the times the WWE used the whole pg-13 to do rather poor storylines/creative work, relying basically on the shock factor to get stuff over rather than making serious efforts. The attitude era had its share of crap.
As far as in ring stuff goes, I think it is a close match -- largely because the IWC people have underrated Austin for YEARS. So I think do Austin was great as an in ring performer. I also think Cena is great as an in ring performer -- in the same league as the greats of this business(including Austin). It is only a close bout because I think both are great.
I ended up going with Cena for this poll, but I think if people chose Austin it wouldn't exactly be wrong or the most preposterous choice of this tournament. I do however think the whole "ZOMG Cena SUX and it is CLEARLY Austin" crowd is preposterous and immature.