shimano factory wheels are cheap for a reason: heavy, difficult to mount tyres as there is no deeper channel in the rim, the freehub skips, and spokes break sometimes. shimano makes a lot of great products, their wheels are not quite there yet (ok-ish for the price though).
as I mentioned the 'extra weight' is almost all in the hubs (about 300g a pair or so vs cheap cartridge bearing hubs with a (rather fragile) aluminium freehub body, which is what you get in most 'lighter' wheelsets). The rims and spokes etc in even basic shimano wheelsets appear to be about the same weight as a lot of other wheelsets, and they dominate the way the wheelset feels.
For the past few model iterations the rims in the cheaper shimano wheels have had a full-width plastic rim tape; this is springy enough that you don't always see the depth of the rim well when the tyre is off. The well itself isn't wildly different from the well in lots of other rims. If your tyres are a tight fit then it is usually possible to fit a narrower/thinner (eg self-adhesive cloth) tape and this gives more slack where the tyre beads sit and makes fitting them easier.
IMHO most hubs ought to be serviced before they are used and this counts double for shimano hubs. IME the freehub bodies are almost 100% reliable (even in the cheap wheels/hubs) provided they are adequately lubricated. It takes less than five minutes to add a shot of the right SFG to the bearings of shimano hubs; this keeps the seals, the main bearings, and the freehub body sweet. If you do that once a year or so, and keep them adjusted properly (*), they will last virtually indefinitely.
If you want not to break spokes, it is necessary to stress-relieve most factory-built wheels. The current (cheap) RS11 wheels use (stupid) straight pull spokes but many older models of basic shimano wheelsets used conventional J-bend spokes which are at least easy to source/replace.
(*) the correct adjustment for any cup and cone hub is of course to have a little free play in the bearings that just disappears as the QR is fully tightened. If there is no free play with the QR loose, the bearings will see an immense (and highly destructive) preload once the wheel is installed.
They are, as you say, not bad for the money; IME most of the possible shortcomings are easy to overcome. [FWIW I suspect that many of the problems that folk experience are provoked by the 'they are only cheap so it isn't worth looking after them' syndrome; this guarantees problems down the line with most equipment....
] The one you can't get over is when the rim is wrecked, it isn't normally cost effective to replace it. Just like lots of other throwaway wheels.
cheers
