here's my take:

Here are points for consideration:
1. Quality - No need to consider resale value, but need to consider maintenance cost

- maintenance cost - Toyota Altis of course, the resale value is a bonus, that is, if you dont mind buying now as the new model is about to be released. Better wait for the next gen.

2. new-Lady driver (owner) - But will also be used by my parents

- I think most cars will be ok for a lady driver.

3. Conservative driving - Is ABS a must?

- ABS is a must for safety.

3. Sub-compact - Sedan

- Vios or Jazz,

The CIvic, ALtis, Mazda3 are all compact sedans.

4. A/T - (are there differences in A/T of different cars? does it matter?)

- A/T is perfect especially for city driving. in my experience, Toyota's A/T is still the best.

5. Mostly city-driving with weekly Pampanga trips

- A/T then!

6. Passes flood-prone areas during rainy seasons (should I opt for bigger wheels, 15" against 14"?)

- consider MPV or SUV na lang.

7. Max 850T including insurance, LTO, etc.

- now I'm confused too! hehe

8. Fuel efficiency (SOHC vs DOHC? Does this affect FC?)

- no

9. Does having sold discs in rear breakes important?

- no,

10. Easy handling (Is the suspension better in Mazda/Ford better than Toyota?)

- or do you mean easy to drive? Altis is easy to drive, Mazda 3 has nice handling.