I never tried upgrading at BB, Radio Shack, etc. so I can't say for sure how long it's been, but I'm pretty sure that was the case when I bought my EVO 4G at launch so it's been at least two years. I think there were people that were still able to get it done on occasion before, but the system they use to handle the accounts is apparently now completely separate between Sprint corporate and other stores.
A corporate store or telesales is the only way to get it done so you'll definitely be paying the $199.99 plus tax. Also, if you don't live in a pretty densely populated area, you might want to make sure the Sprint store you decide to go to is for sure a corporate store because it seems like they're all being bought out by third parties. The only time I ever go to a Sprint store is to upgrade, and it figures that when I went to get my S3 I found out that what I thought was the only remaining local corporate store was no longer a corporate store. (The closest one is now 90 miles away and in a state with significantly higher sales tax so I just ended up going through telesales. At least the shipping is overnight if you're impatient.)