Actually, it is a fair bit of misrepresentation that Saqlain 'lost out' due to injuries.
Everyone's had to deal with injuries at some point or another in a career thats anything more than 4-5 years in the sunshine.
For someone who's watched Saqlain a fair bit, i can say that at one time, he was an even better bowler than Murali and Warne but ironically, the 'doosra' (or the offie's 'wrong un' ) was the downfall of Saqlain, much like how it is becomming the downfall of Harbhajan.
Unlike Warne or Murali, who are wily enough to use the wrong un/doosra sparingly or disguise it well when using it frequently (ie, Murali), Saqlain became over-reliant on them.
He became so over-reliant on the doosra that watching the last 2-3 years of his international career, you could garantee that he'd bowl atleast two doosras per over.
Moreover, Saqlain's doosra was not disguised as well as Murali's is (in terms of action) and once the difference in his action was 'figured out' ( i'd heard Boycott talk about it in 99 series vs India) his doosra lost potency too. Not to mention, his over-reliance of the doosra affected his conventional offspin significantly too- he started losing accuracy in his offspin and his beautiful flight became a flat, predictable trajectory- i am guessing it'd probably because of him focussing too much on the doosra and not maintaining his practice of the off break in the nets as much.
Overall, Saqlain fell off drastically and injury or no injury, his bowling went from sublime to trash. Saqlain i last saw was against India in Pakistan (and i'd be surprised if he hasn't deteriorated further) and he had fallen far enough to be a less accurate and slightly more crafty version of Chris Gayle with the ball.
To answer the question, Kumble is the superior bowler in tests and quite easily so.
People who compare records blindly, in my opinion, fail to understand the dynamics of the game. Spinners rely a lot more on the psychological aspect than pacers, simply because confidence against a spinner pays much larger dividends than confidence against pacers. This fact is easily demonstrated by comparing really accurate pacers with really accurate spinners : say Pollock and McGrath vs Warne and Murali. The latter duo have been taken apart in their 'off days' considerably more often than the former duo.
Where this confidence comes in, is dependent on the overall bowling attack.
To a spinner, it makes a world of difference if they are comming in at 50/3 or 80/1
Having a good pace attack (and Wasim, Waqar, Akhtar are certainly 'as good as it gets') before a spinner makes a huge difference. Warne's average too bloats up when McGrath isnt present in the lineup. And just comparing the two Ws to Srenath and Prasad is an insult to the two Ws. Enough said. As far as tests go, Kumble is easily superior to Saqlain. In ODIs, i'd take Saqlain as the second alltime spinner (behind Murali) - ie, ahead of not just Kumble but also Warne.