I recently built with one of the larger building companies in Perth. I won't name names but you can always PM me

1.) Tradespeople didn't like working for the company because they paid very little and expected the job done quickly. As a result, they would do a hurried job, compromising the quality of the workmanship.
SOLUTION - Talk to tradespeople and you might find some builders that get mentioned in a positive light. This is a long shot and is no gaurantee, but it "may" help.
2.) The builder simply took on too many jobs and was not able to devote sufficient attention to each client. During my construction phase, I had 4 different supervisors. It was a mess! Things discussed with one supervisor would not be passed onto the next so they would often forget where they were at.
Also, the supervisor I had was in charge of 30 homes at the same time. With the pressure and stress of juggling multiple contractors and schedules, it was a sure recipe for disaster.
SOLUTION - Talk to the builders. Ask them how many projects they take on at any one time and how many homes the construction supervisors are in charge of.
3.) Draughtsmen are not architects. If the builder does a custom plan for you, chances are they won't have thought it through as thoroughly as an architect. You may be better off paying a reputable architect to design the house if you are at all fussy about the final outcome.
SOLUTION - Perhaps bring your plans to somebody who can give you a professional opinion on them, or at least someone who is proficient in reading plans. They're technical documents and there are likely to be things you miss - especially if building a house for the first time.
4.) Try and get a feel for how flexible your builder will be when it comes to providing your own fittings, tradespeople, etc. For example, I would want to supply my own tiler next time, because tiling is something that VERY FEW people can actually do well. Tilers need to be perfectionists and now that I've found a really good tiler, I would want to use him everytime.
5. Iif you have a unusual block shape or size, you might wish to check that the builder has enough experience with those types of projects and can show you examples of plans that may suit your block. If they care enough about your business, they will take the time to show you some appropriate plans. A couple of large builders I approached simply said "Oh it'd take me forever to find plans that would work on your block".
In closing, shop around and try to get a few strong reommendations, then speak to those builders and make your own mind up. Or at least get a feel for builders that you definitely shouldn't go near!!
I hope some of this helps

Regards,
Daryl