Ummm no, India were just exceptional against spin in that period. Tendulkar, Ganguly, Dravid, Azharuddin were not just good players, they were exceptional players of spin. So Warne got kicked around by he came up against batsmen who weren't troubled by spinners generally.
This. Warne could've been in tip top form, he still would've been torn to bits by india.
They were good players of spin. But there were factors which meant that Warne didn't face India at his best until his last test series against them.
In his first series Warne was picked before he was ready. He averaged 228 vs India and then followed that up by averaging over 50 vs the West Indies in his next test series. He then started to perform after that until 1998 when his shoulder failed him.
People forget how bad Warne was between 1998 and 2001 while he was recovering from surgery. During that time he took 110 wickets in 31 tests at 35. In that time he took:
31 wickets in 6 tests @21 vs England (career ave 23) (his only better than career average return during this period)
28 wickets in 9 tests @50 vs India (career ave 47)
21 wickets in 6 tests @40 vs NZ (career ave 24)
12 wickets in 3 tests @31 vs Pak (career ave 25)
8 wickets in 3 tests @14 vs SL (career ave 20) (he bowled a grand total of 56 overs in the entire series)
2 wickets in 3 tests @134 vs WI (career ave 30)
6 wickets in 1 test @23 vs Zim (only test)
So we have two hypotheses.
1) That Warne was perfectly fine during this time and the Indians were genuinely just too good for him; or
2) That something was up during this period with Warne.
If we only look at the English and Sri Lankan results, we could easily believe #1. He was averaging around his career average vs England during this time. He did better than his career average against Sri Lanka. But looking closer at that we can see that Warne took the majority of his wickets in Sri Lanka on a turning track where he was out-bowled by Collin Miller. So it's really his results against England that were an outlier here.
To believe #1 we also have to discount the 6 tests vs New Zealand and 3 tests vs Pakistan and 3 tests vs the West Indies where he averaged between 6 and 104 more than his career average against those teams.
The Warne from 2004 was more indicative of the real Warne that other teams had to face during his early and late career peaks. Outside this 1998-2001 period Warne averaged under 24 with the ball, compared to 35 during this period. Taking out his 9 tests vs India during this time he still averaged 30, which was 5 runs higher than his career average. India played Warne well and were fantastic players of spin, but Warne was clearly not his best.
Yes, Murali had statistically better results against India than Warne, but it's clear that Warne only faced them once during his peak. In that time he took one five wicket haul on a road, averaged 30 and was out injured for the best track for spin in the series.
As for ODIs, Warne played two ODIs against India during 1994 and 16 against India between 1998 and 2001. So they offer no insight at all.