I've gotten almost all my preorders from FYE, and never had any bad experiences...they had my AW:DR, MP3, Galaxy, Pokemon Diamond, etc. preorders in store, day one. I prefer FYE over GameStop personally, mainly because I find GameStop more insulting as a corporation.
You'll be fine preordering from FYE, they don't get as many games as GameStop and co, but it balances out because most people preorder elsewhere, thinking 'well this store specialises in games so THEY MUST HAVE MORE'. They've always managed to fill the quota of preorders for major releases around here, and I'm sure your local chain is equally reliable.
As for horrorstories...the only major complaints against them I've heard had to do with forcing customers to buy Wii bundles at launch, the knowledge and attitude of the employees will naturally vary from location to location but at least they aren't pushing merchandise on you every few seconds to protect their jobs. What have you heard specifically?
Anyways, you're worried for no reason, Nintendo doesn't say "THIS IS NOT A MAJOR CHAIN" and ship less games as a result, they ship to meet the number of preorders with a set number of extra copies to select locations if there is a surplus of discs, explaining why it was so hard to get Wiis when they were first released- so many people preordered that there weren't any others in circulation. You have a preorder, so you're going to be the one -laughing- at everyone else who doesn't. If it makes you feel any better, I'm going to FYE tommorow to see if they have Brawl in store, maybe talking my way into getting the game early. I'll let you know what happens.