There are many gaps in your assumptions.
- Who says Wall-E was built at the same time as EVE? Maybe Wall-E was an outdated model at the time of Axiom's departure.
- Who says the Axiom has not updated its technology as it went? For example, the hover chairs may have been created afterwards and not as the initial launch plan.
- Who says Wall-E and EVE were built by the same company with the same quality standards and access to technology? (Edit: they were built by the same company, but given it's the only global company, it stands to reason that the company divisions around the world don't all work with the same technology or standards)
And as the fourth and most important point, there's still their vastly different environments and purposes.
Wall-E is built for tough and dirty work. His design follows that of construction vehicles (link). Tough, built to last, and built to be easily fixed by a mechanic in the field.
We see this happen when EVE rebuilds Wall-E. Spare components were available and easy to swap, because Wall-E was built to be repaired while out in the field without specialized mechanics nearby.
EVE, however, is not built for tough and dirty work. She's not expected to physically interact with rubble day in, day out. She also has no easily replaceable parts and is much more a "black box" in terms of how she is built and how her components operate. Your average Joe plumber won't be able to fix EVE with some spare parts and a screwdriver. When EVE breaks down, the Axiom either has a highly specialized process for taking her apart and fixing her, or may even just scrap her and build a new EVE. EVE is not built to be repaired while out in the field.
Different purposes lead to very different builds. Looking at cars instead of robots, look at the vast differences between a sedan (link), a mining truck (link) and an airplane (link). Very different vehicles, yet they are all vehicles of some sort built in roughly the same period with roughly the same access to technology.