As a student of Latin and Linguistics, in the spirit of fun I'd make the following observations. The pronunciation of Latin, like that of English, is subject to a number of variations. Listen to the BBC news for a week and these days you will hear a wide variety of dialectal pronunciations, none of which are wrong though they are probably not yours or mine. For modern pronuncers of Latinized names we have at our disposal semi-hypothetical classical pronunciations and at least two modern pronunciations used by scholars in different English speaking countries. The linguist in me says, for English or for Latinized names, to use (as best you can) the pronunciation commonly accepted by those in your dialect community, but avoid correcting anyone whose pronunciation may be considered correct in her or his language group. Furthermore, if inconsistency seems a problem, it may be useful to remember that English is rife with pronunciation inconsistencies as noted by Shaw's humorous spelling of fish as "ghoti." (with the [gh] from "laugh", the [o] from "women" and the [ti] from "nation"). I'm sure David's analysis of the long a sound's origin for -ae is correct, but I pronounce baetis "bay tis" as most of my Latinized piscator friends do (though, following Jason and Gonzo I am starting to prefer the term baetids for the little olive buggers). And although bee tis sounds funny to me, I'm not correcting anyone who says it: who knows from where they come? Even so, my classical background leads me to further inconsistency in pronouncing the ae plural at the end of Latin and Latinized words as a long i. Puellae just will never feel quite right to me with a long e sound at the end (or with a long a for that matter). That said, I pronounce (and spell) encyclopedia the way most of us do, and I spell Julius's title Caesar and pronounce its ae with a long e sound. If this solution is one up with which some will not put, I recommend to them the following light reading:
The History of Latin Pronunciation
Allen, W. Sidney. Vox Latina: A Guide to the Pronunciation of Classical Latin. 2nd ed. Cambridge University Press, 1978.
Brittain, Frederick. Latin in Church: Episodes in the History of its Pronunciation, Particularly in England. Cambridge University Press, 1934.
Brittain, Frederick. Latin in Church: The History of its Pronunciation. New ed., rev. and enlarged. Alcuin Club Tracts 28. London: A.R. Mowbray, 1955.
Collins, John F. A Primer of Ecclesiastical Latin. Washington, D.C.: Catholic University of America Press, 1985.
Copeman, Harold. Singing in Latin, or, Pronunciation explor'd. Oxford: by the author, 1990; available from the author at 22 Tawney Street, Oxford OX4 1NJ.
Reviews: Douglas Leedy in Performance Practice Review 5 (1992), 103-8. Lawrence Rosenwald Historical Performance: The Journal of Early Music America 5/1 (1992), 47-50. Gunilla Iversen in The Early Drama, Art, and Music Review 15 (1992-3), 19-22.
Daitz, Stephen G. The Pronunciation and Reading of Classical Latin: A Practical Guide. The Living Voice of Greek and Latin Literature. Guilford, CT: Jeffrey Norton, 1984. [a tape cassette with a booklet]
Duffin, Ross W. "National Pronunciations of Latin ca. 1490-1600." The Journal of Musicology 4 (1985-6) 217-26.
Kelly, H. A. "Pronouncing Latin Words in English." Classical World 80 (1986) 33-7.
Ranum, Patricia M. Me'thode de la prononciation latine dite 'Vulgaire' ou 'a la franc,aise': Petite me'thode a` l'usage des chanteurs et des re'citants d'apre`s le manuscrit de dom Jacques Le Clerc (vers 1665). Se'rie "Musique" ed. Alain Artaud. Arles: Actes Sud, Hubert Nyssen Editeur, 1991.
Scherr, Vera U. G. Auffu"hrungspraxis Vokalmusik: Handbuch der lateinischen Aussprache, Klassisch -- Italienisch -- Deutsch, mit ausfu"hrlicher Phonetik des Italienischen. Kassel: Ba"renreiter, 1991.
Sonkowsky, Robert P. Selections from Vergil, Read in Classical Latin. The Living Voice of Greek and Latin Literature. Guilford, CT: Jeffrey Norton, 1985. [cassette tapes with a booklet]
Trusler, Ivan. The Choral Director's Latin. Lanham, Maryland: University Press of America 1987.
Wray, Alison. "Authentic Pronunciation for Early Music." Companion to Contemporary Musical Thought. Ed. John Paynter, Tim Howell, Richard Orton, Peter Seymour. London & New York: Routledge, 1992: vol. 2: 1051-64
One can also learn much about the pronunciation of medieval Latin from studying the historical development of the Romance languages. Some examples:
Joseph Louis Barbarino, The Evolution of the Latin /b/-// Merger: A Quantitative and Comparative Analysis of the B-V Alternation in Latin Inscriptions. North Carolina Studies in the Romance Languages and Literatures 203. Chapel Hill: U.N.C. Department of Romance Languages, 1978.
Joseph Louis Barbarino. Latin and Romance Intervocalic Stops: A Quantitative and Comparative Study. Studia Humanitatis. Madrid: Jose' Porru'a Turanzas S.A.; Potomac, Maryland: Studia Humanitatis, 1981.
Klausenburger, Ju"rgen. Morphologization: Studies in Latin and Romance Morphophonology. Tu"bingen: Niemeyer, 1979.
Wright, Roger. Late Latin and Early Romance in Spain and Carolingian France. Liverpool: F. Cairns, 1982.
Wright, Roger, ed. Latin and the Romance Languages in the Early Middle Ages. London and New York: Routledge, 1991.
"He spread them a yard and a half. 'And every one that got away is this big.'"