As I've already said, injections cause great hormone level variations. That alone is reason enough for me to believe it's reasonable to at least consider that maybe it's sub-optimal/risky. After all, hormones aren't naturally released once a week; they're fairly constant. Also, some doctors (who I definitely find convincing) argue that maximum feminisation is obtained with a very slow and steady increase in E dosage, then a dose as stable as possible. Injections do the exact contrary, don't they?
Plus, an injection is generally a pain to do, and it's not even a habit you can take on daily like pills. I'd tend to think that it's really, really easy to be late, forget a shot, etc.
And depending on how and where you inject it, the way the hormones circulate through the body could differ. Depending on the tissue or area or deepness, I think the rate at which the hormones go to the blood stream can vary. Such an unstable regimen (one week huge and steep spike; the other, a softer spike...) doesn't feel 100 % healthy.
Of course, I don't have much to back myself up, but that's what I believe.