OK, you guys knew this was coming... I just have to jump in here. I'm going to keep my opinion
very narrow-reaching... that is to say, based solely on what I've witnessed with my own two eyes, here close to home. I think anyone trying to really compare Storm Cat to A.P. Indy is barking up the wrong tree. Let's not compare apples to oranges... let's recognize what each sire does best... what each one can bring to a breeding program... then focus on which one fits best into a particular program based on it's goals and expectations.
The A.P. Indy son that I know well

is a gorgeous animal... perfect conformation, beautiful mover, just a perfect picture in my book. A real "looker." The Storm Cat sons that I've seen are not anywhere near as pretty and are
not conformationally correct, although everyone knows that doesn't necessarily stop these horses from kicking butt on the track!
So, let's say you have a mare that matches exactly as well with the A.P. Indy line as she does with the Storm Cat line (I know, not going to happen, but work with me...) Here's how I see it:
If you want an early maturing speed horse who will probably be successful early-on and who will more than likely win you some return on your investment relatively quickly, but may burn out and be done with racing at an early age (all your fire and glory early on, so to speak)... go to the Storm Cat line.
If you want a later maturing horse who probably shouldn't even bother to start until it's a 3YO, who will probably want more distance but who will probably also get better with age and be successful for a longer period of time
IF YOU UNDERSTAND THE LATE MATURING-DISTANCE LOVING THING AND ACTUALLY DO RIGHT BY THE HORSE IN THE BEGINNING INSTEAD OF PUSHING IT TO RACE BEFORE IT'S READY... go to the A.P. Indy line.
Some want the early 2YO superstars, some are willing to wait for a horse that will do well at distance and get better with age... thank goodness for variety!
I think there's a place for both lines, depending on your goals. We bred to a Storm Cat son and got a colt who is a 2YO this year. He is one that we plan to race as a 2YO, because his sire's get seem to burn up the track at 2 and 3 but then they typically tail off and are done... this horse NEEDS to race early or we've probably wasted a good opportunity with him.
We have a lot of offspring of a certain A.P. Indy son, and they get to play and romp and be horses until they're 3, then they go into training... and we expect them to start doing well as LATE 3YOs and get better as 4YOs, 5YOs, etc...
If you have an understanding of what the offspring should do and train them accordingly, you should be able to succeed with either line. Now, I'm fully aware that there is another 50% of each horse's pedigree to consider in these situations... but since this is a comparison of stallions, I'm throwing out the bottom side for the sake of this arguement.
If I were breeding for the "big sales" hoping to attract a buyer who was looking for a 2YO superstar, I would go more with the Storm Cat line. But, as a small breeder in a regional market who breeds to race and sell (but sell privately) I prefer the A.P. Indy line.
I hope to have fun and make money with our Storm Cat line colt, but for the most part, I'd rather have horses that may be successful for 5-6 years on the track and then be marketable in other careers. Or, if a horse that I breed doesn't make it to the track, I want other options open... such as H/J, dressage, eventing... people don't want crooked legged or knock-kneed or "not-so-pretty" horses for this type of thing, no matter who the sire is!
I've heard a lot of talk about "small feet" and "bad feet" in the A.P. Indy's... I've not actually seen that myself, although I'm not discounting the experience of others. None of ours have foot problems... they're actually as a rule very correct, well-balanced, good looking individuals who stay sound. Interestingly, our "smallest hooved" broodie is from the Halo sire line, and our broodie with the "worst" hooves is from the Gallant Man line. Other than that, we've got pretty good feet out here, and we've not had any hoof problems with any of our Indy foals.
Again, this is just my personal (long-winded) opinion as to what fits best into our personal program... there are other people with vastly different goals who's programs work better with other bloodlines. I don't think anyone can argue against the statement that both Storm Cat and A.P. Indy have their place in the market and they are different places... but each one is important in the overall scheme of things.