I don't think there is a little hierarchy problem in general (this is why I never regarded it as a real problem; it is a somewhat mild issue only in the most minimal SUSY theory).

The origin of the little hierarchy is that in the MSSM, at tree-level, the Higgs cannot be heavier than 90 GeV or so (see hep-ph/9709356 for a still relevant review). So in light of the LEP bound (115 GeV) one has to get a pretty decent contribution (to the quartic coupling) from loops. To make the loops sufficiently large one needs the stop to be somewhat heavier than the top. But that comes back to hunt you since it destabilizes the Higgs mass. Typically, for a Higgs around 120-130 I believe one would have to live with tuning at the per mil level (more optimistically, one could perhaps get 10^{-2}).

However, innocuous additions to the MSSM allow for heavier Higgs particles at tree-level. For instance, one can add a singlet (this leads to the so called NMSSM) or one could add an additional gauge group that is broken at the TeV scale (this enhances the quartic coupling through new D-terms). One can cook models where there is virtually no tuning whatsoever.

Note that there is no model independent bound on the stop mass, it could easily be 300-400 GeV in some scenarios. Therefore, in the presence of additional tree-level terms in the Higgs potential, there is no tuning.

(It should be added, though, that in many models beyond the MSSM one looses gauge coupling unification...)

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