Mechanical problems with agitators are rarely as simple as steady bearings or larger shafts. Either approach may solve the problem or make it worse.  You have identified a couple of advantages and problems for each option, but others are possible.  From the information you have provided, I can only guess at possible solutions.
 
However, from your description, the problem may be in the rigidity of the mounting.  If both agitators are having similar problems, it is likely that the support structure is at least contributing to the problems.  To make any recommendation for or against the options you mentioned would require a much more thorough analysis than a simple description of the agitators.
 
Detailed dimensions and drawings would be needed to completely evaluate the strength of the agitator impellers and shafts.  The drives and supports are potential sources of problems.  Even your process conditions need to be examined to establish the loads on the agitators.  Other mechanical problems such as natural frequencies for both the agitators and the supports can cause motion problems.
 
For an independent start, an article entitled, "Consider Mechanical Design of Agitators," by Fasano, Miller, and Pasley, in Chemical Engineering Progress, August 1995. pp. 60-71, has some good information on mechanical design of agitators and supports.

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