How to make Apple Maps work for transit directions and finding businesses:
I've gotten myself to a pretty good solution, so I thought I'd share.  Mine is NYC-based, but the POI solution will work almost anywhere, and the transit one should work in most major cities in the US (which are the only places transit's likely to be a must-have.)
Here's the really short version:
Download Where To? for  business listings ($2.99) and Embark Transit for subway directions (free, if they cover your city).
Both plug directly into Apple Maps app, and plug its two major gaps.
How to find businesses and points of interest:
Dowload Where To? on your iPhone.
Yes, it costs $2.99, and there should be good, free solution, but there isn't, and it works.   Where to? will let you just click from categories to find common business types near you without typing:

And, if you're looking for something specific, you can search, and its database is not just limited to chains and common stores (I tested it by searching for B&amp;H, a well known, but single-instance NYC electronics specialty store.)
You can see the results in a list, or on a map.  Importantly, once you find somewhere you want to go, you can click on a little &quot;right curve ahead&quot; icon (it's also the app's icon) to get directions there, using either apple maps (which can then provide turn-by-turn directions since Where To filled the gap of finding the business), or using other apps you may have installed (MotionX, TeleNav, etc.)
There's also a 0.99 in-app purchase that lets you put locations on a camera picture, augmented reality style.   This probably more cute than useful.  It might be functional in dense cities if the compass worked better in them, but you can try it free to see if you like it first, so there's not much harm.
How to get transit directions:
Dowload Embark Transit on your iPhone.
Embark is free, pretty solid, and has apps that cover:

Boston
Chicago
Philadelphia
London
NYC
Washington, DC
San Francisco
Caltrain
NJ Transit
Metra
LIRR

It's got the full map of the system, but can also route the best path between two addresses and give you step by step directions of what station to walk to, where to transfer, etc.

And it works underground, as the data is stored locally. It doesn't cover every city, and it's not good at finding much without an address (like business names), but because it plugs into maps, and we now have a good way to get POIs there using embark, that's not a big deal.
Here's how to use Embark (or any 3rd-party transit app) from maps:

Install the app on your phone.
In Apple maps, click the &quot;right turn&quot; icon that goes to the directions screen - it's in the upper left corner of the app.
On the top of the directions screen, click the &quot;bus icon&quot;
Enter your Start and End (if they didn't pre-fill), and click &quot;route&quot;
You'll get the choice to use any installed transit app - in this case, it'll show you Embark, and if you click it, it'll open with that route pre-filled.

Yes, it's all a little more kludgey than it has to be.  But it works.