Comparing the best trail bike examples of each.
26″ – Unstable without slack HA, doesn’t climb well on steep tech unless quite steep ST angle, manuals easy, stiff wheels, easy to get perfect position (low bars etc), nimble and fun but gets out of control sooner, light weight.
29″ – Stable, longer wheelbase (plus and minus points), more climbing grip/ability (longer rear centre), more difficult to manual, more effort (ability?) required to maneuver, boring at low speeds but ultimately more control at higher speeds (wheelbase/BB drop), noticeably less energy required (contact friction/tyre deformation), wheel flex unless expensive CF options used, better suspension performance for similar travel (roll centre).
Latter is faster no doubt in my mind. Former is probably more fun especially at lower speeds.