For myself, I generally go with the middle level improvements ('advanced' this-or-that). They are almost as cost-effective as the entry level, and you aren't as likely to replace them later. Note that an entry-level mine on a mountain will do you more good as a medium-level mine on plains, but cost less.
However, there is one reason not to do so: war. If the enemy is likely to pillage your improvements, consider using entry-level stuff (so it takes him longer to damage you), or Mega-level stuff (so you can park defenders on that tile).
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