So why are skill-based games so hard to develop? Are they harder to
develop, or is that just a myth perpetuated by the lack of developers
willing to undertake skill point systems? Due to my inexperience as a
game developer, I won't even gesticulate on this topic, and let the
developers answer the questions for themselves:
EVE Online's Matt Woodward:

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I don’t think that skill versus level is an issue here
– the difference comes when trying to balance skills versus
trying to balance classes. My gut feeling here is that, for a given
total number of available skills/abilities, classes will always be
easier to balance simply because tying specific skills/abilities to
specific classes mathematically reduces the number of possible
combinations. That said, even within classes with at least some degree
of flexibility you’re still going to see optimized builds in
most cases. I’m honestly not sure it’s possible to
achieve “perfect balance” without making the
variations effectively meaningless and/or soullessly, boringly
mathematical. Maybe if you had some incredibly cool tool which could
calculate the damage/tank/other combinations for every possible build
and flag up the ones which were potentially problematic you might be
half-way to solving it, but you might also just be giving your balance
developers a nervous breakdown – finding problems and solving
problems aren’t the same thing!
I have a sneaking suspicion that the best way to resolve this sort of
issue is to design a series of optimal builds and then build the system
around those builds. If you have some choices which are meaningful and
tweak specific builds towards different playstyles without having a
large impact on power, and other choices where there’s a
subtle but compelling optimal choice, then you’ll end up with
a system that has “bad abilities” designed in that
no sane person would use, but you also end up with a system that gives
the appearance of choice while also (hopefully) giving you a stable,
balanced set of “flavor of the decade” builds that
you can take as given and design around. It’s kind of a class
system masquerading as a level system, and it’s pretty
underhanded, but it might at least get away from constant power swings.
Until you try to create new loot sets, of course…
Fallen Earth's Lee Hammock:
I think they are always harder since so many more possible combinations
of abilities exist and the current role structure favored in MMOs
(tank/healer/DPS) begins to break down under the myriad
possibilities. At that point you have to re-teach people how
to play MMOs to some extent and depending on how well you do that, you
may get a ton of bugs that aren’t bugs but communication
failures.
As for “build of the month” issues,
that‘s going to happen no matter what you
do—regardless of if you have a class-, level-, or skill-based
system. People are going to develop a build they think is the
best no matter what you do. You will have thousands of players and many
fewer QA people, and your players will think up combos of items,
skills, and abilities that never occurred to you or your QA.
It is impossible to think of all the abuses your player base will find,
so you have to concentrate on finding the most egregious
problems. This leaves lots of smaller issues unfound that
your players may use to create their ideal builds. When these
arise you have to consider whether they are playing as intended. If
not, what parts of the game allow such builds to dominate.
I’m not a big fan of reducing the power of a build because
it’s effective, but instead trying to find other weaknesses
that make that build effective. This may not always be
possible though and sometimes things need to change.
Earthrise's Atanas Atanasov:
Skill-based systems are hard to balance because they place a massive
amount of options in the hands of the players with very little or no
limitations at all. To ensure balance, such systems require an
incredible investment in time and testing, and even then the final
result never reaches perfection. Yet, the key to the success of MMOs is
not balance itself, but the feedback from the designers that respond to
the evolution of the game and provide fast and proper changes that
cater to the expectations of the players. Instead of allowing players
to take advantage of unbalanced character builds, changes should be
made to ensure that the design team responds before such issues could
reflect on the whole game.