Really? I don't find conceptual and technical difficulty of considering (co)homology theories determined by spectras/infinite loop spaces like K-theories and cobordism theories, study of stable homotopy theories, spectral sequences, triangulated categories etc. to be much smaller that the difficulty of algebraic geometry. As I said, I find them both to be really abstract and mysterious.
Many concepts from algebraic topology can be applied to algebraic geometry after appropriate redefinitions. These new tools seem harder to use than originals. For example I find it technically more difficult to work with étale fundamental group than with a topological fundamental group. Similarly cohomology of a topological space looks simpler than cohomology of a scheme with coefficients in a sheaf. There are many similarities but working with schemes and sheaves is more troubling (at least for me). This of course can follow not from intrinsic difficulty of the subject but from my ignorance and inappropriate intuitions.
