I know a few people who had series 2 for their exams and were still being accepted by BA and easyJet (The 2 airlines that really care). If you've failed more than 5 exams then I would certainly consider it. A few in my course regretted passing the "last sitting last exam" situation and finishing with a poor average etc. You'll also find your second time round way easier too, so it wont be as bad as you think. I've witnessed too many cadets try and apply to the airlines and then get stopped in their tracks because of the ATPL's so it's worth sitting a series 2 with fewer fails and a better average. Rather than series 1 and X fails and X average.
For the record, this is just my opinion and what I've witnessed when I took my ATPL's at a large ATO 2 years ago.