Just a few thoughts...
When you are talking about shooting on 35mm film, the issues can be:
1) Standard 2X anamorphic implies shooting 4-perf, so the cost savings of shooting 3-perf spherical cannot be implemented.
2) Generally anamorphic photography is finer-grained than Super-35 cropped to 2.40 because of the larger negative area used for the final scope image.
3) Anamorphic lenses are generally slower, heavier, and less available to rent (and more expensive to rent) worldwide, which is why many people go to Panavision, who have one of the largest inventories of anamorphic lenses. But generally your anamorphic lenses are going to cost double what your spherical lenses cost, or to put it another way, the most expensive spherical primes to rent (something like Zeiss Master Primes) are about the same rental as the cheapest anamorphic lenses on the market.
4) The anamorphic lenses are somewhat handmade, meaning that few sets are made year-by-year and they each have certain optical idiosyncrasies, so it is hard to mix and match sets compared to modern spherical lens sets.
5) Most anamorphic zoom lenses are rear-adapted spherical zooms and therefore tend to not be as sharp as anamorphic primes, nor as sharp as spherical zooms, and they tend to be slower than their spherical counterpart (a T/2.8 11:1 Primo zoom becomes a T/4-5.6 lens in the anamorphic version, for example). Panavision recently has made some front-element anamorphic zooms however.
6) Most front-element anamorphic primes started life from elements from a spherical lens and you can crudely think of an anamorphic lens as a spherical lens with a wide-angle adaptor, just that the wide-angle effect only happens horizontally... the reason I mention this is that, as you can imagine, the anamorphic elements add to the size of the front of the lens. If someone ever took a set of Master Primes, which are already on the large side, and anamorphized them with front anamorphic elements, they would be gigantic, which is one reason why Panavision Primo anamorphics are so huge since they started with regular Primos as a base. And the JDC anamorphics were or are fairly small in comparison because some of them started out as older Cooke Panchro lenses. This is one reason why some of the newest anamorphic lenses are being designed from the ground-up rather than start with existing lens elements.
7) Some anamorphic lenses have a poor minimal object distance -- most E Series Panavision anamorphics, for example, only focus down to 5'.
8) Anamorphic distortions that people either love or hate tend to decrease as you stop down.
9) If you are shooting digitally, then the benefit of getting finer grained with anamorphic over cropping spherical to 2.40 is sort of lost. And any resolution improvement from using a larger negative area compared to cropped spherical (with in 35mm can help anamorphic photography look sharper than spherical even when the anamorphic lenses aren't sharper) is also lost if the anamorphic lenses are used on a 16x9 sensor or 16x9 recording format, in which case horizontal resolution will be lost when cropping the sides to get a 2.40 image (because a 2X optical squeeze on a 1.78 : 1 sensor gives you a 3.56 : 1 image otherwise). This means that the only real reason at this point to shooting anamorphic is because you want the unique optical artifacts and distortions, not because of greater image quality.