Well to answer the question about their reputation, no, they do not have a good reputation. However, I think the bad reputation is completely unfounded. A lot of changes for the better have been made in the last year or two that most people either don't know about or don't believe. I've heard nothing but trash from either former students or people with no first hand knowledge, but I've never heard anything bad from any current students. Current students all seem to agree that it is a great school, and I really wish people would give them a chance before they go and bash their reputation further. The biggest complaint I hear is about the price. FYI, the price is competative with all the other big name schools. They are simply more truthfull up front about how much it will actually cost. Another complaint I hear is about the old aircraft and facilities. Well, they are safe and they get the job done. What more do you need? Having old aircraft keeps the costs down. It is extremely expensive to operate at a major international airport, and if they had brand new planes and facilities, they would have to charge us upwards of $100,000 for training.
I plan on attending Sierra starting next fall(ish). What sold me on Sierra was the following.
1. Location. I will get plenty of actual instrument time without having to fly through thunderstorms. I will get fewer cancelations because of weather. I won't have to endure 150 degree heat and 500% humidity. The bay area is a really fun place to live (but expensive). I'll be operating in Bravo and Charlie airspace - good experience for an aspiring professional pilot.
2. Instruction. Sierra has higher standards for their instructors, thus I will both get better instruction and I will be a better instructor. In fact, another complaint I hear is that their CFI program takes too long. Well, the reason it takes so long is because they expect you to learn more.
3. It just feels like a good fit.
4. Personal reasons.
What I suggest you do is trust your instinct. What was your overall feeling about the academy after the tour? Visit some other schools and compare. Do some research on your own before you decide you won't go just becasue of some horror story someone (who probably has no first hand knowledge) tells you. All schools have their horror stories by the way. Look into all stories you hear (good or bad) to check their validity.
Good luck.