I think the main thing that upset people is that Bioware is notorious for ignoring bug reports and customers complaints. The Bioware forum is pretty draconian and any criticism toward Bioware is often met with a ban.
For example, there have been a large amount of report that certain copies of the PC version of ME3 will not play any sound because there's some incompatibility issue with Realtek sound drivers. There is still no official response from Bioware regarding this issue, which is pretty unacceptable considering this is such a big game release. The fail character transfer is just another thing on top of all of these other issues.