First, the interface between the systems will be difficult if you have different platforms. Even for the file transfers between the systems, you will end up writing script, which will take some development time.
Secondly, you may find it difficult to get any consulting help, since there are not many Basis consultants with Unix and Windows NT expertise. For the same reason you will end up paying more consulting costs.
A third point to consider is that SAP Enterprise Portals (EP6) is on Unix, and if you decide to install portals later, it will have a better interface with Unix systems than NT systems. So even if you have some cost savings initially, you may end up with issues and difficulties if you decide to go with different platforms.
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