In short, there is no help to offer. You have no control over the quality of image that FTM downloads. If it really irks you, send in your feedback in writing to the FTM folks. Maybe you can persuade them to give us control or simply to download the best quality available.
For what it's worth, I understand wanting the best quality available. Before FTM 2012, I used to manually download everything just like you. I too was annoyed that the automated downloads weren't as good as the manual downloads.
This is a question of cost-benefits. When you compare the image you downloaded vs. the image FTM downloaded, is there a significant difference in readability? Does that difference justify the time necessary to manually download and then import to FTM, link to source citation, etc. If the difference in readability isn't significant, is there a significant disadvantage to the image not being the best available? These are questions you have to answer for yourself.
From my perspective, the organizational work is identical whether you download an image manually or have FTM get it. You still have to write a caption, date, description, transcription, and notes. That's enough work for me. I've chosen to accept the lower quality images, because I find the quality to be good enough, and I like not only that they're downloaded for me, but also that they're already linked to the source citation. For me, the time I save outweighs not having the best image available.