As far as I know, the word "species" can pronounced either as spee-sheez or as spee-seez. I understand that neither of these is incorrect: they're just two different ways to say the same thing. I also know that the second one is pretty much only used in the US. Not being a speaker myself, I'd like to know: is this a regional variation, or is it just something that depends on the speaker?
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The Received Pronunciation (which is the "British Standard", in a way, the one which is also exported) suggests the first one "spee-sheez". Source: Oxford English Dictionary
The US pronunciation accepts both. Source: Macmillan Dictionary
Probably the biologists would use the second one, as internationally there is more consensus on that variant. Also, it comes from ecclesiastical Latin, where the /spetʃies/ pronunciation was used.
There is more likely a professional/academical difference in pronunciation, than a geographical one, as the word is not everyday language.
As an American, I pronounce it similar to [spee-sheez]. However, the "sh" sound in species is different from how I pronounce the "sh" in most other words. I am not sure if this is normal or not for an American. I pronounce the "sh" in species with my tongue in the normal position for "s" with the back of my tongue near where it would be for saying the y sound.
I always pronounce the normal "sh" sound with my tongue between where it would be for saying an "s" and saying a "y".
It pretty much depends on the speaker, aside from the general factors you already mentioned. An older pronunciation that I don't think is used anymore was /ˈspiːʃiiːz/ ("spee-shi-eez"); this stems from the same variation in syllabification that affects words like fascia (which can be pronounced /ˈfeɪʃiə/, /ˈfeɪʃə/, /ˈfæʃiə/, /ˈfæʃə/).
The pronunciation with /s/ is a bit irregular from an etymological standpoint, although it actually doesn't have anything to do with Ecclesiastical Latin.
However, in other words, such as rabies, scabies, and series, it is pronounced with a single vowel /iː/. This is actually an irregular correspondence between Latin and English pronunciation: the OED says that the N.E.D. (1903) listed a trisyllabic pronunciation for rabies, and the N.E.D. (1912) listed /ˈsɪərɪiːz/ for series. I suspect that the pronunciation of these words has been affected by analogy with plural words that end in monosyllabic -ies such as cities. A re-analysis of rabies and scabies as plural forms seems likely since there are a number of other disease names in English that are morphologically plural (such as measles). Series also seems similar to a plural in meaning (some people, although I think mostly non-native speakers, back-form a singular serie).
The OED still lists a trisyllabic pronunciation for caries, but all the other dictionaries I've checked give the two-syllable pronunciation.
In words like species, facies, superficies, it's actually pretty regular for the i to not be pronounced as a separate syllable, but we would still expect it to palatalize the preceding consonant, resulting in /ʃ/. The pronunciations with /s/ are irregular, and would have to stem from some process of analogy like I mentioned for rabies, scabies and series.