Haven't talked about either of these in a good long time (and as you can see by my recycling the Sylar poster below, I don't have much left in the way of Heroes-based posters) so I'm going to just ramble on for a bit.
So, who here figured it would come down to this after 5 years? That Heroes is barely clinging to life, with a very mixed season at best, and a lot of moves that come off more as desperate grabs for attention, is a surprise in and of itself. However, coupled with Smallville, which just seems to keep going and going despite having long since snapped the cables on the suspension bridge of disbelief, is astounding. As you can guess, I have a few thoughts about why this has happened, and what it says about each show.
Now, the first thing we have to note is the rather large difference in approach. Smallville follows the traditional format of a genre show - a series of episodic adventures with a few sub-plot arcs that transition to the main story over time, while Heroes follows the currently popular method best known on Lost of Mega-arcs that play out over long timescales, with very little in the way of status quo. This difference manifests itself in pacing: Smallville gets away with little beats in every single episode (i.e. there's one story beat about Lois and Clark, one about Clark and Chloe, one with Green Arrow and another character, one about Clark coming to terms with what he has to do, a beat resolving the villain of the espisode). Heroes? Has maybe three beats total per episode, if that. So while you might, might get the long term payoff in Heroes if you stick around long enough, you get lots of little payoffs in an episode of Smallville - more bang per hour of watching, if you'll buy that metaphor.
One of the story beats in particular is essential (in my opinion at least) to a superhero story regardless of medium is crime-fighting and saving lives. Smallville has radically improved in this regard over the last couple years with depictions of Clark regularly saving people other than his supporting cast (Lois, Chloe, etc.) and starting to deal with criminals who aren't just the bad guys of the individual story arc. Contrasted with Heroes, which usually offers a total of one "Big Bad" villain per arc, and usually 2 or 3 flunky villains tops for a whole 10-20 episodes. Also, outside of Hiro performing a random rescue or two and Peter Petrelli's stint this season as Super-Paramedic, you don't see a lot of these so-called "Heroes" helping people who aren't integral to the plot. Chew on that for a bit and see how it affects the message of the show.
Now, let's talk about the big moves both shows have made, whether out of a genuine desire to shake things up, or a last mad dash to avoid cancellation. With Heroes, several prominent cast members have been jettisoned (or had their character arcs reduced to virtually nothing), and a major revelation has changed their world forever. In addition to this, the audience is now being asked to suspend disbelief enough to buy Sylar's attempt at redemption. Now, I can't fault the Heroes writers for this; Zachary Quinto is arguably the biggest draw of the cast, and they need a reason to keep him around that doesn't make other characters look even more pathetic for not dispatching the show's biggest villain for the past four years. But it is a big stretch to buy for a series that tries very hard to want to take the idea of superheroes in a real-world context seriously.
Smallville, on the other hand, has ditched reality to embrace the fantasy of the DCU, integrating more and more of the spectacle that the 70+ years of DCU publishing history has to offer, and the results have been a mix of great (Zatanna) and laugh-out-loud silly (Hawkman's cosutme is just terrible, and Stargirl's is worse). One imagines that the writers just decided that there was no way to make this realistic without making it drab (or being accused of stealing ideas from Heroes) and just decided to take full advantage of the cameo opportunities.
So, when we contrast Heroes, with it's long-game plan, and dedication to trying to keep to realistic ramifications, and Smallville's episodic comic-bookiness, where do you stand? For me, as bad as some of the elements can be (Clark - just put on the tights already) I have to stand with Smallville on this one.