Take a look at Warne's performances from his 98 shoulder injury onward.
Firstly he had what was, all things considered, his poorest series against India outright. He was carrying an injury (and this is widely documented... yes he was fit to play, but he was not at his best, and was due to break down), but he was a strong time in his career and was taken apart brilliantly.
He took 10 wickets @ 54.
After that he played an Ashes series for which he was not fit, having missed a significant amount of cricket with his shoulder problem, and only played 1 test, taking 2 wickets @ 55.
He then toured the West Indies, was so woefully out of form that he was -dropped- from the test side, and took 2 wickets @ 134.
He was in and out of both the test and ODI teams throughout this period, and following his shoulder problem he developed other injuries, most notably to his spinning finger, which would also require surgery in the future and sideline him.
He had two series in which he bowled only a little on his return, but did decently in both of them, taking 8 wickets against Sri Lanka (over 3 tests!) and 6 against Zimbabwe in one game, at cheap averages.
When India and Pakistan toured in the 99/00 season in Australia, Warne was available to play, but he was unfit, had bowled just 200 or so overs in test cricket since the India tour in 98 (in two years), and was bowling the worst of his career. He worked through a solid but unspectacular series against Pakistan, who are usually his bunnies, averaging 30, and then got belted by India, taking 8 @ 41.
He was then sidelined with another injury, which caused him a miss a significant part of Australia's record winning streak and the whole 00/01 home summer, before making his comeback with an average tour of New Zealand, taking 15 @ 27. He was finally getting over his long run of injuries at this point, and would eventually get back to his best, though he would not dominate anyone as he had until he toured Pakistan in October 2002, over a year later.
He then went to India, playing them for the third time in the 98-2001 period, and was once again belted. During this entire period, he struggled against all opposition, not averaging under 25 in any series in which he bowled 100 overs, and in fact averaging under 30 only against New Zealand. He averaged 33, 32, 33 and 31 overall year-by-year from 98 to 2001. In the 14 years that Warne has played test cricket, he has averaged over 30 only six times, four of them in this period, and one of the others being his debut year.
His test average rose from 23.82 to 26.62 in this period, and then levelled out as he gradually returned to his best, with a decreased range, having lost his wrong'un and his flipper, and having needed to rethink his bowling. When he next played India, he performed servicably well.
The point of all this, is that while it is true that Warne has struggled against India, the fact that he played them at times when it was most difficult for him to bowl at his best is not irrelevant, or simply making excuses. India have played Warne very well, and chances are he would probably have struggled aaginst them anyway, but not anywhere near as much as he did, particularly in 99/00 and in 2001.