There may be many reasons, why an instance is slow. It's not very clear form your question, what is slow exactly, but I would like to suggest reading the following articles first:
The number one reason that FishEye/ Crucible is running slow is because the application hasn't been tuned properly. A lot of tuning FishEye requires some trial and error and most of the time it requires a wholistic approach and not any one thing. That's why it's so important to read the above articles and make sure you understand the various tunable parameters (heap size, CPU, initial/ incremental indexer threads, polling vs hooks, etc..) that will allow you to get the most out of your machine and the application.
It's also worth noting that if you're running FishEye/Crucible in a VM indexing of your repositories will certainly be much slower than if it were on a physical server. I/O throughput is very important to indexing performance.
Last but not least, there is always a chance that your environment is at fault as well (network, disk speed, disk space, file descriptors, I/O throughput, etc.). It's important to check if any of these could be the cause.
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