This was true for cross-class skills in 3E as well (the only difference is that it works with exclusive skills in 3.5E). The only exclusive skill that it seems potentially unbalanced for is UMD, and probably only for non-spellcasters (in 3E, you would have been able to do horrible things with Tenser's Transformation, but I'm pretty sure that got fixed in 3.5E).
There are a bunch of other 3-class combinations that do what you want which involve expert, human paragon, or both. These may be overly trivial...
I would take the SRD wording to imply that familiars can't gain HP from polymorphing (since their hit points are explicitly independent of hit dice, why should they depend on Constitution?). By the same token, they should gain hit points from their master polymorphing, just as they would if their master did anything else that changed his Con.
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There are a bunch of other 3-class combinations that do what you want which involve expert, human paragon, or both. These may be overly trivial...
I would take the SRD wording to imply that familiars can't gain HP from polymorphing (since their hit points are explicitly independent of hit dice, why should they depend on Constitution?). By the same token, they should gain hit points from their master polymorphing, just as they would if their master did anything else that changed his Con.