This is an old question but just to say that the dumpwallet command has been added to bitcoin core. This will give you all the private keys in a text format.

I hate to be that guy, but you should really take another look at pywallet. Your problems may be specific to Joric's pywallet, which hasn't been updated in awhile. There is a better-maintained fork of pywallet by JackJack.
If this was the version of it that you already experienced, you could always try the web interface by running:./pywallet.py --web and then navigating to localhost:8989/ in a web browser.
You did however request a command line way of doing it, which with jackjack's pywallet would look like this:
./pywallet.py --dumpwallet --datadir=DATADIR --wallet=WALLETFILE --passphrase=PASSPHRASE
The --passphrase option may have been the issue you ran into with pywallet, since it is necessary for dealing with encrypted wallets, but it isn't in the readme (not really sure why that is).
Anyway, pywallet really does seem to be your best bet for what you're trying to do. If you are having issues using it, feel free to include information about these issues.

Beside that I don't understand your problem with PyWaller, like Eyal suggests, you can use the standard Bitcoin software for this as well, although this method will be a little more time-consuming.

I suggest doing the following for every wallet.dat file you have:

1. Backup your current wallet.dat file.
2. Copy the old wallet.dat to your Bitcoin directory.

3. Open up a terminal and run the bitcoind daemon:

   bitcoind -daemon

4. Retrieve a list of all the addresses in the wallet:

   bitcoind listaddressgroupings

5. For every address you want the private key from, dump it:

   bitcoind dumpprivkey <bitcoinaddress>

6. Stop the daemon before changing the wallet.dat file:

   bitcoind stop

This should give you all the private keys you need and you can import them to any wallet you would like.

As suggested by the other response. You can use pywallet just fine. Since you require the dumping of many wallets and would like a CLI solution, then a simple bash script + pywallet will do just fine.

This is not by any means tested (i.e. backup all the wallets involved), but should do just fine:

Bash

#!/bin/bash

echo "Enter directory with all the wallet *.dat files live:"
read walletdir
echo "Enter passphrases for all the encrypted wallets in directory:"
read passphrase

for i in $walletdir/*.dat; do
    pywallet.py --dumpwallet --datadir=$walletdir --wallet=$i --passphrase=$passphrase
done

Batch (Not my strong side)

@echo off
set /p walletdir=Wallet directory?:
set /p passphrase=Passphrase?:

for /r %%i in (*) do pywallet.py --dumpwallet --datadir=%walletdir% --wallet=%%i --passphrase=%passphrase%

Also if you'd like to isolate any information within the JSON dump itself you can surely do that too. I'm not exactly sure the anticipated output of --dumpwallet as I am not a user of pywallet, but I believe you can edit the pywallet.py code to change

print json.dumps(json_db, sort_keys=True, indent=4)

to

print "\n".join(private_keys)

In conclusion doing those 2 things will print out a long list of all the private keys to all the addresses to all the wallet files.

Disclaimer - Once again, I have not tested any of this

If it's fewer than 10 wallets, just copy them into bitcoin-qt's configuration directory one-at-a-time and transfer all the bitcoins to a new wallet. It would take you about 10 minutes to do it.