A few suggested enhancements that I believe have been raised elsewhere before, and may even be in progress, but logging here for posterity:
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Allow commissioners to set a uniform renewal date for their entire league during each offseason. (If I recall correctly, football can already be run this way, but obviously no reason that it wouldn’t also be useful for baseball.)
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A league notepad where any custom rules, links, or other info with a useful life longer than the average message board post can be stored.
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Possibly more controversial: Make any owners claiming abandoned teams in the offseason pay roster fees up front. Discourages owners that will claim teams on spec, then drop if they can’t manage them into a favorable position before the season.