Geordie,
Firstly,let me be totally honest with you. I have no personal knowledge on the view
of UK border agency in these days. My experience is now already 4 years old.
I can tell you that you will need very detailed evidence. In the case I know of there were also character references and letters of support etc from professional people in Philippines.
You appear to be fairly swtiched on concerning the processes.
But just to recap:-
1.Annulment - If you have the time (probably 2 years average)
and the money (average P200,000) this process will null and void the marriage and enable remarriage.
2.Separation - This does nothing to change the state of marriage really.
A judicial separation in the Phils is also time consuming (the court will do nothing until 6months after filing the petition) not to mention very tedious and very full of pitfalls on elegibility. Not as expensive as annulment. The courts may want to try any possible reconcilliation and try to fully settle any possible claims on conjugal property.
In both cases the other spouse cannot be seen (or believed by the court)to be colluding.(tricky)
For unmarried partner visa you will probably already know that you will be required to prove with evidence that you have been ".. living together as if you were married or in a civil partnership for at least two years"
On the question of proving marriage has permanently broken down then from the evidence that you have already you have a very good chance of success provided the evidence is substantiated from 1994 up to the time you began living together for at least two years.(should really include the period time leading to the visa application)
Anyway, hope this helps in some way