This will be really really really really really bad as coming from experience of being affected by the first Skyway construction and Skyway Stage 2, commuting from Manila to the South has really been one of the most hated experiences of my life.
And since the first Skyway has been built a decade ago and the volume of cars, trucks, buses & motorcycles has been out of control over the years.
Here are 10 Reasons why it would be the apocalypse for motorists:

1. There will be construction accidents, and it will happen given the accidents I've witnessed.
2. It won't be finished on time (who knows anything can delay it)
3. Get ready for more road rage incidents, hoping no one would get shot.
4. Lots of cars, trucks, buses and motorcycles(I wish...) will be breaking down due to the long traffic jams causing more traffic jams.
5. Flooding? Construction debris(sand, cement) and drainages don't mix.
6. The first and second skyway only affected SLEX (a 6 lane tollway), Stage 3 would be affecting multiple main thoroughfares, roads, avenues, etc....
7. Typhoons wrecking havoc on the Construction Site/Equipment, the cranes would fly off like twigs.
8. If the project becomes over budget or other financial reason for delay.
9. When politics intervene (bound to happen :P)
10. And when more NEW vehicles add to the traffic (Manila please start a Car Scrapping / Recycling Program like Malaysia or Singapore)

Bonus: Earthquake, seeing that even Japan's Earthquake Proof Elevated Expressways can buckle I'm not discounting Skyway...

On the brightside, Los Angeles has nothing on Manila's Carmaggedon.