So, first of all, let me start by saying that I took a quick glance at the current version of Shadow's patch which seems to be 1.71. I still need to double check this and go through things more thoroughly, but it does appear he actually fixed at least some (possibly all) of the major problems that originally existed. This included things like wizards not being able to use scrolls the module author expected and changing the implementation of Empower Spell to be incorrect.
Given that, the downsides of using his patch appear much smaller. That said, it still generally seems the benefits are pretty minor as well.
Caveat to the above: my understanding that a builder with the CPP could do a lot more, but we're talking strictly about a player using it right now.
the reasons given for not installing it are inaccurate to put it nicely.
Well, let's see...
I'd think of stuff like a visual glitch or something else that doesn't affect gameplay if I were to think of a "minor bug", whereas CPP fixes some, I think, big ones.
There's a *ton* of stuff like this:
- Slay live (sic): added missing impact damage visual effect
- Inflict Wounds: visual effect changed to less intrusive one
plus spell school or innate spell level changes that the vast, vast majority of people will never notice, let alone even care about.
For example, some feats (like Trident Weapon Focus or Circle Kick) are useless without CPP and not really fixable by a module builder.
Here's a question: how many people even care about Trident Weapon Focus working? It's a martial weapon that's flat out worse than a spear (a simple weapon) in every way? I think it literally may be the most useless weapon in the entire game. Pretty much everything else has at least SOME reason to use it...but not the trident.
Most modules and many PWs don't even have tridents, either due to them not existing prior to 1.67 or because they're so worthless.
Circle Kick just fell into the category of "useless, don't take" along with other feats like Dirty Fighting and Improved Parry (which isn't even counting all the feats that technically work correctly but are still so terrible no one ever takes them). It's been that way for 13 years or whatever and people have adjusted to the fact that many feats just are...really bad. Fixing it is nice, I guess, but it only affects monks...and then only monks fighting unarmed (rather than with a kama)...and the bonus winds up being pretty minor eventually anyway.
I don't disagree that something like Shadow's patch is needed to fix those. I just question the actual value of the fixes.
I think it'd be useful for a new player not only because such a player is not aware of what feats/spells/skills might be bugged, potentially breaking his build, but also because the original descriptions for these are often misleading, and sometimes outright false. With 1.71 patch you can be much more certain that in-game descriptions will tell you the truth.
Just my three cents on the matter. 
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And like Whizard said, in many modules this doesn't even hold true.
If a module uses custom AI? Write off many of Shadow's fixes there.
If a module uses a custom spell system (like Aielund and the EMS)? Write off Shadow's fixes there.
Or how about some basic stuff? Let's say I think Firestorm should hit all targets, not just enemies, and thus I alter the script as a builder (and I'm not using Shadow's patch). You play my module and you have Shadow's patch. Suddenly Firestorm is doing up to 40d6 damage again because I didn't fix that bug in my modification but my modification takes precedence.
Speaking of Firestorm, an amusing story. When I was balancing my module Siege of the Heavens, I assumed that caster focused Clerics and Druids would be using Firestorm as one of their main nukes since it did 40d6 damage. Using Shadow's 20d6 Firestorm makes those much weaker. That said, Clerics can still buff up and reasonably melee while Druids can still shapeshift (which was improved) so it isn't the end of the world...but it wasn't my goal.
To be clear, Firestorm doing 40d6 was completely and utterly a bug. But it still means that if I want caster Clerics/Druids to be as viable as I intended, I either need to buff their spells in general or "fix" Shadow's fix. And a player trying to be a caster Cleric/Druid using the CPP would be not having nearly as much fun as I intended and will probably feel rather weak.
Other examples of these problems exist, like how Arqon had to fix EMS when Savant told him how making it so AoEs didn't destroy placeables wound up breaking parts of Savant's Aielund Saga. Arqon wound up making it so Lightning Bolt *only* would affect those.
The general point is that a module not written with Shadow's patch in mind (which includes modules written before his patch even existed) might run into problems in unexpected ways because the author was relying on certain behavior/bugs/etc that Shadow changed/fixed.
So, yes, historically I've been very wary of Shadow's patch. Like I said, it does seem he fixed some/all of the major problems...but other stuff does remain (like the whole previous section). I'd probably even be willing to say that if the author used Shadow's patch and the player is using Shadow's patch that there's essentially only benefits (potentially some major ones if the builder took advantage of a the stuff in Shadow's patch)...but, well, that simply isn't the case most of the time.
