Hi there @bloomlwold - I feel the same way about the "advice" the game keeps giving you. It's almost a mini-game - try to ignore bad advice without raising your blood pressure.
The megatowers - oh boy, seems like a good idea. It's a balancing act on top of a balancing act. Just like you can't really get sims from one city to commute to another city (and come back), the megatowers seem to be their own contained thing. I have had the same struggles with balancing the levels. I have been "successful" for a while, but inevitably there will be a time where you have conflicting messages on the different towers. A residential level will say "Not enough work" and the mall level above it will say "Not enough workers".
If you decide to try again, don't mix wealth levels in the same megatower. Make sure the land value around the megatower matches the land value of the sims. Plop parks of appropriate wealth level all around the megatower. If shoppers can't get to their commercial shops they will go to parks and you can keep them happy there. Remember that low and medium wealth will use city transportation like streetcars and shuttle buses, but high wealth always drive, so you'll want to tailor the area to keep everyone walking. Also, Megatowers have 3 entrances. Make sure you have roads connected to all the entrances, to help with traffic flow.
The biggest complaint I have with megatowers is that they are very slow to react to changes. I think that's why you get the conflicting messages between the levels. The fastest way to deal with issues on a level is to demolish the level. That can be very expensive, though, because the first couple of levels that you built are probably the ones that have the issue. You can't demolish the first level without demolishing all the levels above it. You don't have to demolish the base, though, and the base doesn't have any costs associated with it, so you can demolish everything and let the city run. I think there's actually a bug that keeps the income from the megatower even after you demolished it, so a mini-exploit to gain cash without managing the megatower.
I know I sound like I'm discouraging megatowers. They can be useful if you manage them, and don't feel too bad about demolishing levels every once in a while. Personally, I prefer to building an Arcology Great Works for more workers. But an Arcology doesn't give your city income, so megatowers might be the better option depending on what you're trying to accomplish.
Good luck on whichever you choose. Happy Building!
