Here are some thoughts, gathered from reading many texts about algebraic K-theory. Let me start with some historical remarks, then try to give a more revisionist motivation of the plus construction.
First of all, it's true as you say that the already-divined definitions of the lower K-groups made it seem like the higher K-groups, whatever they might be, bear the same relation to the homology of GL(R) as the homotopy groups of an H-space bear to its homology groups; thus one is already looking for an H-space K(R) whose homology agrees with that of GL(R), in order to define the higher algebraic K-groups as its homotopy groups. This line of thought is amplified by the observation that the known partial long exact sequences involving lower K-groups seemed like they could plausibly arise as the long exact sequences on homotopy groups associated to fibrations between these hypothetical H-spaces.
So it may already at this point be natural to try to turn GL(R) into a H-space while preserving its homology, which is what the + construction does. However, the facts that:
1) the + construction ignores the admittedly crucial K_0-group; and
2) in any case, at the time there were very few lower K-groups to extrapolate from in the first place
mean that perhaps the above is insufficient motivation for defining and investigating such a seemingly ad hoc construction as the + construction.
However, we can bear in mind that Quillen's definition of the + construction came on the heels of his work on the Adams conjecture, during the course of which --- using his expertise on the homology of finite groups --- he was able to produce a (mod l) homology equivalence
BGL(F) --> BU
when F is the algebraic closure of a finite field of characteristic different from l. Now, BU is a classifying space for complex K-theory (in positive degrees), so its homotopy groups provide natural definitions of the (topological) algebraic K-theory of the complex numbers. Furthermore, by analogy with the theory of etale cohomology (known to Quillen), it is not entirely unreasonable to guess that, from the (mod l) perspective, all algebraically closed fields of characteristic different from l should behave in the same way as the topological theory over C. (This was later borne out in work of Suslin.) Then the above (mod l) homology equivalence adds further weight to the idea that the hypothetical K-theoretic space K(F) we're searching for should have the same homology as BGL(F). But what's more, Quillen also calculated the homology of BGL(F) when F is a finite field, and found this to be consistent with the combination of the above and a ``Galois descent'' philosophy for going form the algebraic closure of F down to F.
That said, in the end, there is good reason why the plus construction of algebraic K-theory is difficult to motivate: it is, in fact, less natural than the other constructions of algebraic K-theory (group completion, Q construction, S-dot construction... applied to vector bundles, perfect complexes, etc.). This is partly because it has less a priori structure, partly because it ignores K_0, partly because it has narrower applicability, and partly because it is technically inconvenient (e.g. for producing the fiber sequences discussed above). Of course, Quillen realized this, which is why he spent so much time working on the other constructions. Probably the only claim to primacy the + construction has is historical: it was the first construction given, surely in no small part because of personal contingencies --- Quillen was an expert in group homology.
In fact, probably the best motivation for the + construction -- ahistorical though it may be -- comes by comparison with another construction, the group completion construction (developed by Segal in his paper "on categories and cohomology theories"). Indeed, Segal's construction is very well-motivated: it is the precise homotopy-theoretic analog of the classical procedure of going from isomorphism-classes of f.g. proj. modules to the Grothendieck group K_0 by formally turning direct sum into a group operation. To get this homotopy theoretic analog, one "simply" carries along the isomorphisms in this construction (c.f. also Grayson's article "higher algebraic k-theory II"). The connection with the plus construction comes from the ``group completion theorem'' (see the McDuff-Segal article on this subject), which, under very general conditions, allows to calculate the homology of such a homotopy-theoretic group completion in terms of the homology of the relevant isomorphism groups. If you look at the group completion theorem in the case of the space of f.g. proj. modules over a ring, you'll see the connection with the plus construction immediately.