1) Trainees will not see the same variety of schools that they would via a university-based PGCE route.
As much as this may be true to some extent all School Direct trainees will be expected to spend time in more than one school as required for obtaining QTS. In fact, some school consortiums are able to provide their trainees with experience in a greater variety of schools.
2) Trainees won't get the important reflection time away from school that they would if they were following a university based training route.
I don't know how this will work for those trainees not gaining a PGCE, but I know that one day a week I will be training in curriculum and professional studies away from my school with other student teachers. This will give me the opportunity to meet with other students, like I would do had I been at a university, and discuss issues and share experiences with them.
3) There won't be a strong enough focus on theory and academic study.
Again, although I don't know quite how this will work for non-PGCE trainees (presumably in a similar way to the non-PGCE GTP route) but so far I am under the impression that there is still a strong academic focus to my course. I will be attending university for 2 weeks next month with full days of curriculum and professional studies. I will still be required to complete academic assignments in order to gain my PGCE and I am still expected to study the same texts as the university based PGCE courses.
As far as I can tell so far, many of these criticisms of School Direct would also apply to Teach First, SCITT or the previous GTP.
I understand the concerns related to applications and the knock-on effect this is having for university providers and this is certainly an issue that can't be ignored. That said, in the cases where the School Direct training route also leads to the award of a PGCE I don't see the downside or the risk to teacher quality.
The variety of provision for School Direct across the schools and universities involved is yet to be seen, some with PGCE, some without, some with a wider variety of experience than others. I guess what I'm saying is when making judgements about School Direct this variety must be kept in mind and we mustn't tar all of the training providers with the same brush.