1) The stock was closer to $57 in January 2000 if you average the trading days, not $35 (high in Jan was $64 at the end of the month, low was $42 at the beginning of the month).
2) They generated $22.9b in sales and $9.4b in profit in the fiscal 2000 year. Ballmer inherited about a 45 PE ratio, which is a massive multiple for a company with a $425+ billion market cap. An impossible multiple to maintain at that size I'll note. Just ask Apple, their PE has imploded from 35 to 60 several years ago, down to 9 recently (now 12 or so). Does that make Cook a terrible CEO, the fact that it's very likely impossible for him to build a trillion dollar company? No, he inherited a growth monster that is rapidly slowing down. Welcome to the law of big numbers.
3) Sales have increased from $22.9b to $77b so far under Ballmer. And profits have gone from $9.4b to $21.8b for fiscal 2013. For a company that was already the largest software company in the world, that's a spectacular operating performance. Meanwhile they've returned 40% of their market cap in cash to investors.
The notion that any company can dominate all industries simultaneously, such that Microsoft was going to own search, social and mobile is absurd to put it very lightly. The notion that Microsoft can just magically stop all future giant companies from existing, is equally absurd.
I don't think he was a great CEO, but your bashing is completely off target. You're criticizing Ballmer for basically not being a trillion dollar company with $100 billion per year in profit by not being a combined MSFT + GOOG + AAPL + FB. That makes no sense.