I mentioned this in another question, but just because the morphological inflection is disappearing, that doesn't mean the subjunctive mood is actually disappearing from the language. Just like when most of our verbal inflection disappeared (now it's "I go", "you go", "we go", "they go"), that doesn't mean we lost verbs for first person singular and plural, 2nd person, and so on.
Nohat's short answer gives the main point — if 9 out of 10 times the form looks identical to a MUCH more common form, then over time things might converge and regularize. A linguist would call this "paradigm leveling". Less common words and structures tend to regularize faster than more common ones (which is why words like "to be" and "to have" are irregular in so many different languages). The subjunctive is rare and not that distinct in English, so it is in trouble.
We see the past subjunctive form only in "to be", but we see the present subjunctive in the third person singular form of any verb — it has no "s" at the end like the indicative form.
So, this is of course subjunctive:
If I were ten years younger... (often said "If I was...")
But this is subjunctive too:
So be it.
It's important that he arrive on time tomorrow.
There are a bunch of examples here that include this other kind of subjunctive. This is just anecdotal but I haven't noticed this one disappearing as much.
Is this a general trend in related languages? Well, in Swedish this seems to be happening. In German one subjunctive form is used all over the place, and the other is used pretty much just in newspapers and journalism in general, but it is at no risk of dying out (it has legal implications akin to those that make the word "allegedly" so important in English journalism).
I don't think that it's the same prefix as much as it is the remnant of a number of different grammaticalised pre-fixings. Most of them seem to have happened during the period when then curious admixture of French, Viking Danish, Anglo-Saxon and a sprinkling of Gaelic were distilling themselves down into the various dialects of Middle English. The spelling's kind of arbitrary, but a is the letter we tend to use when a word starts with a schwa that's flatter than we'd represent with a short e.
English was essentially an unwritten language during that period (and the population essentially illiterate), so it could be a time of great flux. A lot of words were repartitioned. All one became alone, the n sound migrated from the ends of words like mine and thine to become the initial (and previously non-existent) consonant of words (especially eke names -- thine eke name also became thy nickname) and so on.
As with a lot of what happened during this period, what we have now in the language is mostly what was present in and around London when the orthography was fixed by printing. Many of the a- words that one recognises as quaint regionalisms today (like a-hunting) were standard in dialects that did not, themselves, have the good fortune to become the standard themselves.
As for new words, well, printing (and general literacy) sort of put a stop to arbitrary movement of word boundaries. A question was posted here earlier asking about the meaning of "grab a hold", and it didn't take long for somebody to reply that the phrase was actually "grab ahold" (something my spell checker has decided is a problem). I would bet that "grab a hold" or "take a hold" (hold being synonymous with handle, as preserved in hand-hold) was the original phrase. They sound the same, and if you hear a hold often enough without seeing it written down, there's no real reason why you might not think of them as a single word.
Best Answer
Wikipedia (citing A history of the English language by Richard M. Hogg and David Denison) suggests that the loss of gender in English was "due to a general decay of inflectional endings and declensional classes by the end of the 14th century" as evidenced by increasing use of the gender-neutral identifier þe (the or thee).
"Why" is, of course, a difficult question to answer here. It seems that whatever pressures had influence over the evolution of the English language, the net result was a loss of accents, inflections and declensions. The above sources indicate that grammatical gender is like another form of inflection or declension, so it gradually disappeared from the language at the same time.