by next week we hope to eliminate linked servers for structure comparison (quickly followed by removing them for data comparison). Most problems with linked servers have been removed but for aforementioned problems and other issues we are going to remove them.
Current version is 2.18 which has a ton of features added and fixes made since this review was written and is 4-10x faster again.
Interestingly enough removing linked servers has allowed us to make the product faster not slower. The de-linked version will be faster by several magnitudes again.
version 3.0 will be coming out shortly with re-designed interface, command line, internal scripting engine and hopefully SDK. stay tuned!