A lot of people find it somewhat surprising, but Einstein's initial formulation of special relativity was in a paper, On the electrodynamics of moving bodies, that makes very little reference to the Michelson-Morley result; instead, it is largely based on the symmetry of electromagnetic analyses in different frames of reference.
From a more modern perspective, there is a strong theoretical case to be made that special relativity is, at the very least, a strong contender for the description of reality. These are beautifully summed up in Nothing but Relativity (doi), but the argument is that under some rather weak assumptions, which are essentially
- the homogeneity and isotropy of space, and
- the homogeneity of time, plus
- some weak linearity assumptions
you are essentially reduced to either
- galilean relativity, or
- special relativity with some (as yet undetermined) universal speed limit $c$,
with no other options.
To get to reality, you need to supplement this theoretical framework with experiment - there's no other way around it. The Michelson-Morley experiment is, of course, the simplest piece of evidence to put in that slot, but in the intervening century we have made plenty of other experiments that fit the bill. From a purely mechanical perspective, the LHC routinely produces $7\:\mathrm{TeV}$ protons, which would speed at about $120c$ in Newtonian mechanics: it is very clear that $c$ is a universal speed limit, because we try to accelerate things faster and faster, but (regardless of how much kinetic energy they hold) they never go past $c$.
If you want something from further back, this is precisely the reason we developed the isochronous cyclotron in the late 1930s and then switched to synchrotrons back in the 1950s - cyclotrons require particles to keep in sync with the driving voltage, but if they approach the speed of light they can no longer go fast enough to keep up. We have upwards of eighty years of history of being able to mechanically push things to relativistic regimes.
If you wish for an answer inscribed within "experimental physics as of 1888, minus the Michelson-Morley result" then, as I said, the symmetry properties of electromagnetism (which are directly compatible with SR as derived from $v\ll c$ experiments, but require aether theories to make sense in galilean relativity) were plenty to convince Einstein that SR was the right choice.
Edit:
As pointed out in a comment, Einstein's original paper does make some reference to Michelson-Morley(-type) experiments, in his second paragraph:
Examples [like the reciprocal electrodynamic action of a magnet and a conductor], together with the unsuccessful attempts to discover
any motion of the earth relatively to the “light medium,” suggest that the
phenomena of electrodynamics as well as of mechanics possess no properties
corresponding to the idea of absolute rest.
However, apart from this small nod, he makes no substantive references to the aether or its equivalents: the paper starts with the relativity postulates (based on the constancy of the speed of light), uses those to construct special relativity (as pertains transformations between moving frames, and so on), and then builds his case for it on the transformation properties of the equations of electromagnetism: these provide the deeper fundamental insight that underlies the symmetry of analysis of electromagnetic situations performed on different moving frames of reference.