In some respects this is the most important facet of game design. I'll give you a simple example of what I'm talking about that relates to Eve-
Because players can kill NPCs and refine items dropped by said NPCs, and even worse yet, be allowed to kill drone NPCs in the drone regions that drop nothing but ore to be refined into raw materials (minerals) used to produce items in Eve, this marginalizes the importance of mining and the mining profession in Eve.
I doubt that any of you reading this would have ever thought I'd be making a post about the importance of mining eh? The many parallel material streams in Eve harm mining and it's central importance to the Eve economy and overall gameplay. If a player can simply 'mine with guns' and produce material more efficiently than using traditional mining skills and ships, then what is the point of mining at all?
Most players want the game to be easier. Not easier for everyone, just easier for them. "I want more officer NPC spawns" one might say. Ok, now what? Everyone has more officer spawns and now the items dropped by officers are devalued to the point that they're worthless. Not a good idea.
Players are highly risk-averse. They'll go to great lengths to avoid being killed, even if it means increasing the effort and time required by a factor of a thousand to reduce their risk from 5% to 0%. This group of playes is collectively known in Eve circles as "Carebears".
These types of players are the worst, most harmful type of player for the game. They create a static market environment and generate large influxes of currency without the reqired consumption to maintain a balanced economy. This is why we see PLEXs at their current prices, and rare faction mods selling in the billions (the ones that are most important to running missions in Navy Ravens that is). But I digress, I'm getting off the main point here.
Every ship, every item, every system in the game needs to have purity of purpose. The more refined and specific each item or system is the happier the player base will be because they won't be frustrated by having to use a tool that isn't up to the task at hand and they somehow have to make do with something second rate. The less overlap we have in design will allow players to make better choices with their gameplay and will provide greater player satisfaction when they accomplish their task because they won't be fighting poor design in order to accomplish their end goal.
Evidence of poor design can be seen quite easily in usage statistics. If an item or system is even a few percentage points less effective than the most effective item in it's class, the usage statistics will be drastically reduced when compared to the number one best performing item.
However, most of the time poorly designed systems aren't so obvious with respect to being easily defined by skewed statistical data. POS warfare is an easy target. Cumbersome, poorly implemented, frustrating, most players that I talk to on a regular basis despise having to manage POSes and their built in requirements for 0.0 warfare.
I know that CCP recognises that POS warfare needs to be addressed, and indeed, I'm sure it's a priority for them and knowing CCP they won't take half measures and change a few things when they can take the time and effort to do it right and completely revist the design and build it up from scratch instead. But again- purity of design. Let's rethink what is the best system for controlling space, and what is the best system for providing players with individually owned and operated remote outposts. One systems requirements are wildly different from the others. This is key- in all games, but most particularly with MMOs, systems need to be able to scale effectively from the individual to tens of thousands of players, and when a system breaks at one end or the other then it's time to build seperate systems to accomplish both envelopes so that you don't end up with something that is ungainly and unoptimised.
Purity of design- when (as an example) all the weapon options for short range turrets have been 'balanced' so much that they all do nearly the same amount of damage, have nearly the same range and other performance characteristics then all you end up with in the end is what I like to call "oatmeal": a big pile of mush that all looks the same, tastes the same and basically is the same. Conservative design and redesigning the game to average out performance issues between items and game systems is the quickest way to kill a game in my opinion. Right now CCP is enjoying continued success with it's business but I believe that is due in large part to the fact that they have no real competitor in the marketplace. There is no other product on the MMO landscape that even comes close to providing the unique combination of factors that Eve has. As soon as someone delivers an MMO that has the open ended player driven environment of Eve with a similar setting (scifi, space based etc.) and a PVP centric core gameplay CCP will have to really improve it's product or it'll be left sitting on the sidelines.