Things happen on different time scales. I think he had nothing to do with the dot.com bust, but had everything to do with the jobless "recovery," and his "stimulus packages" (though they do work, short term) were nothing but band-aids.
What he did to science in the U.S. is reprehensible, and if this isn't a result, we will be feeling many of its effects for many years to come. He legitimized backward thinking (read the Republican War on Science)
Even stalwarts of the Republican Party approached him about maintaining U.S. competitiveness in Science education, but he brushed them off like they were a nuisance (I saw one instance, personally, and heard of many others). He simply doesn't seem to care (and may even be harboring some form resentment).
In addition, his administration continually stoked peoples fears (that should be obvious), which is never condusive for progress. Terror alerts are not conducive for business trips, and less face-to-face time is bad for morale and efficiency.
War can create many jobs (which is good for the economy) but it also creates uncertainty and fear, and drains peoples morale (which is bad for the economy).
The "you're either with us or against us" attitudes created real divisions between people who worked together well before (I know many personal instances, and this is ont the type of thing people keep statistics on)
Funding for research programs was funelled based on ideology, rather than effectiveness (part of the "we took office, and now lets screw the oter side as much as possible, mentality"). Again, people don't keep statistics on this type of thing. But anecdotes among scientists abound.
He also essentially played the role of the prototypically spoiled rich-kid as a leader (read Imperial Life in the Emerald City) and legitimized that style of thinking (many modern CEOs are like that, and it was hard to knock them off of their magical thinking, and the belief that problems will go away when you ignore them).
I have experienced the stagnation in innovation personally, yes.
Note: a lot of the critisism leveled at "Republicans" falls squarely on the Bush Administration itself.
I am rather conservative leaning, fiscally, but the Bush adminstration sucks not because of their fiscal policy per say, but their mismanagement of morale.
The effects of psychology on the economy are immediate. Psychology can cause runs on banks that "ought" to be solvent, sell-offs of company shares that "ought" to be worth more, and various other things... and these affects happen fast and in the short term. The constant morale lowering effect that the Bush administration has had is, IMO, horrible.