So, if you want to go for a complete set, in the order NPPL(M), flexwings --> NPPL(M) 3-axis, NPPL(SEP), JAR-FCL PPL(SEP), you'd be looking at a total bill of about £8k, (plus, which I forgot to put in before, licence issue costs to the CAA). Not a bad way of going about it!
Essentially the route I took, apart from starting on 3-axis. I learned on Shadows, bought a share in a Jabiru (a combination that will no doubt identify the training outfit for GtE!) and subsequently found converting to 152s for the then-new NPPL SSEA to be pretty straightforward. A small-ish extra cost of that route is the need to sit what are a rather similar set of exams once for microlights and then again for the NPPL SSEA.
Being confined to the UK while flying Group A then motivated me to convert to the JAR PPL, coupled with the desire to join a friend's N-reg group which meant getting something to base an FAA licence on - all things that fit under the 'flexibility' heading in rustle's excellent summary earlier in this thread.
If you had a flexwing microlight licence and then wanted to add an extra rating in the sense of night, IMC, twin, IR etc., then clearly you'd have a large extra cost to bear since you'd need the JAR PPL as a minimum. If you wanted to add even the simplest extra 'rating', the Night Qualification, there would be nothing to gain by doing the NPPL SSEA along the way since it doesn't support the qualification you're after and still costs you money for examiner's test and CAA licence issue fees. You would need to plunge straight into the JAR PPL.
In the very best case you'd get 10 hours credit for your microlight experience (10% of your total, limited to a maximum of 10 hours) and you'd be well-placed to pass in the minimum time since you should already be comfortable with navigation, radio and so on. Depending on the time of year, you might be able to gain the night qualification during the course too, so let's say a best case of 35 extra hours (plus Class II medical costs) for a 100 hr+ flexwing pilot to get a night qualification and the appropriate licence to attach it to.
Of course, on the aircraft ownership side, most of the extra ratings will mean that you can't use a PFA aircraft to exercise them, so you'll have to raid the bank account again for a CofA, FAA or similar machine.
If I'd known when I started that I'd want to end up flying internationally in a Group A aircraft it would have been more cost-effective to have gone straight for the JAR licence, but for me it was a case of wanting to dip my toe in the water without too much outlay (it cost me about £2,500 all in in 2001 for the old-style microlight licence) and then paying extra to add extra flexibility from there.