Jeremy Jameson created an article series which talks about serious problems he ran into when using the variation feature. Unfortunatelly I cannot comment his articles directly as he disabled anonymous comments - and my blog is not on MSDN but on TechNet so I cannot login in MSDN so I have to provide my comment here.
1) Incompatibilty between OOTB variation feature and OOTB content types
The correct solution for this problem is to create a custom site definition template which already uses the correct content types. Adjusting the content type of a page will indeed lead to problems in the content deployment and migration API which is used by the variation feature.
A custom site definition template should be defined for all customized sites and the site should then be propagated with this site defintion template rather than adjusting the content type afterwards.
Background info on the problem: when propagating a site through the variation feature the site definition template used to create the source site is used to create the destination site. This means the default.aspx page will be created based on the content type in the site definition. When later the variation features trys to pair up the pages in the source label with the pages in the destination label it sees the different content types and this causes the problem.
Using a custom site definition that has the correct content type for the default.aspx configured will avoid this problem - and will also reduce the overhead for authors as they don't have to change the content type for the pages over and over again.
2) Enabling of content types on destination labels
Jeremy complains that the variation feature does not enable content types on the Pages library in other labels. This issue has been identified as problem in MOSS 2007 and a hotfix for this issue is currently in the works and should be available short after release of Service Pack 1.
[Update 2008-02-19] The fix for this issue has been included in Service Pack 1
3) Performance Problems when populating the variation
This has been reported by a couple of customers and the product group is currently investigating the issue. Additional indices as outlined in the article are currently not supported as already mentioned by Jeremy.
[Update 2008-05-21] Two hotfixes for this issue have meanwhile been released as KB 952698 and KB 952704. Both hotfixes are required to address this issue.
4) Attempting to create a new variation label after creating a large number of sites and pages results in an out-of-memory error on the server
This issue has been identified as a problem in MOSS 2007 and a hotfix for this issue is currently in the works.
Background info: we identified that the variation feature holds SPSite/SPWeb/PublishingWeb objects of opened sites during the propagation for caching purposes. At the end these objects are properly disposed but if many sites have to be propagated the amount of memory can be to much on 32-bit machines. On 64-bit machines with more virtual memory per process this problem would not cause the variation feature to fail. The hotfix being developed will address this as it will dispose the SPSite/SPWeb/PublishingWeb objects earlier and if required recreates them later rather than caching them in memory.
Be aware that contrary to the statement from Jeremy only part of this change will be included in SP1. To completly address this issue you need the hotfix which will be available shortly.
[Update 2008-02-19] The hotfix for this issue has meanwhile been released as KB 941274