I don't think I've met my quota for answering/counterpointing interesting Wavinator questions as of late, so here goes :)

To me, there is both a correct, legitimate way of adding/extending gameplay in this fashion, and a forced, idiotic implementation, see also the examples you mention. Since the latter is rather uninteresting and the reasons behind it so blatantly superficial (i.e. 'give us more money' in virtually all mentioned cases) I won't waste time on discussing it. What I will talk about, however, is option A.

IMVO, the now-ubiquitous reloading mechanic found in modern shooters serves as a textbook example of how such a technique can add a lot of useful depth to otherwise extremely simple gameplay mechanics. In truth, I think the consequences of adding this are really way more far-reaching than many would think at first glance, as they extend far beyond the initial "I get this many shots before I need to wait a bit before shooting again." The primary effects are obvious, having an effect on pacing (to be more specific, the periodic insertion of brief downtimes in which a player is unable to retaliate against attacking foes) and providing another scale by which an arbitrary value can be assigned to the possession of a particular dealer of metallic death, though the latter is of more primary concern in competitive multiplayer. First and foremost, this fixed (and, in most cases, considerably smaller) limit on the number of shots fired in any particular span of time encourages players to come up with and execute plans with the primary goal of causing opponents to waste ammunition. While such techniques could obviously be employed in games that did not have such a feature, (say, Quake) any potential benefits were almost as a rule a lot further away and indeed could be mitigated entirely (at least in theory, if you actually did this you'd likely be gibbed on the spot in practice) by the 'victim' camping ammo spawns. As a direct result of this, you've added feinting as a viable, useful and rewarding tactical option. Not only must players be able to react and aim quickly, they must also be able to think on their feet and be able to weigh the potential short-term benefits of opening fire on a real or perceived threat against more long-term consequences of potentially being vulnerable while in a difficult future scenario.

On a semi-related note, similar ideas can be applied as a means of balancing out weaponry with an otherwise excessive damage output capability, i.e. sniper rifles and similar. Once again a player needs to be able to weigh the benefits of attacking another against the cost of expending valuable chances to defend him/herself against future threats. Additionally, the impetus to both identify and remove high-value targets is also increased somewhat. While our hypothetical sniper may be able to set up a kill shot on one of two currently-visible enemy players, he/she now might need to consider which one of these two targets is more valuable, as only one can be taken down.

Now, with all this being said, I think arguing whether or not adding what basically amounts to wait timers before you can shoot again is necessarily the best method of instilling elements of higher thought into twitch games is most assuredly outside the scope of this discussion; just off the top of my head also implementing unwieldy spread patterns and similar also strike me as ways to deal with this problem (though it also bears mentioning that the environment may also play into this, either enhancing the effect or nullifying it and further complicating the issue) though obviously coming with their own set of questions to be answered. I'd also like to state my awareness of limiting ammo, period, as a means of introducing the kinds of metagameplay mechanics I've discussed above, and counter it by reminding that introducing this secondary, typically smaller limit makes the consequences more immediate *and* more frequent, thus bearing more player concern. Additionally, it also has the side effect of forcing players to start off on slightly more even footing in most cases-- having a massive ammo reserve won't save you from an empty clip currently in your weapon, even if the other guy doesn't have more than whatever his mag size is :)