PPTP and L2TP use MPPE for encryption, which means RC4. RC4 is, for all intends and purposes, broken. It's the underlying mechanism for WEP, for example. It can rekey frequently, but RouterOS doesn't expose parameters for tweaking that.
So where does that leave you? Depends. How valuable is the data you're trying to protect? If it realistically isn't all that valuable then RC4 might be 'good enough'. Does any of the data fall under minimum encryption requirements? For example, are you in the US and are you transmitting payment data or something to do with health care? If yes, RC4 is right out.
If you want or need strong encryption then IPsec is the only way to go. Is it a pain with RouterOS? You bet. Shame, that. If it was me I'd still use IPsec, just on a different platform. There are plenty of free (other than the stock x86 hardware) solutions available. And while painful it can absolutely be done with RouterOS - I'd still prefer even that to PPTP/L2TP.
Fewi, you know I respect all the hard work you put into these forums, but as a security and crypto nerd, I have to come to the defense of RC4. RC4 is very misunderstood, so it catches a lot of bad press because it is either not used properly, or weaknesses are found in the key-generation systems used to initialize it. The reason there are so many attacks against protocols using RC4 is because RC4 used to be the gold standard for EVERYTHING.
The RC4 keystream cipher is not insecure as long as it is initialized properly with a good key. The weakness with WEP was the result of improper use of RC4. When first initialized, the beginning of the keystream needs to be discarded because it leaks info. With WEP, this initial block of weak data was not discarded, which lead to the weak IV problem and eventually the Korek and PTW attacks.
As for PCI compliance, the problem is not with the use of RC4, but rather the use of 40-bit keys to initialize it. 128-bit RC4-SHA and RC4-MD5 are currently accepted as strong encryption for SSL/TLS by both PCI and HIPAA.
You are correct that PPTP is somewhat broken, but here again the problem is not directly with the RC4 cipher, it is with CHAPv1 using a 40-bit key, and CHAPv2 creating a initialization key that has less than the required 128-bits of entropy. MPPE using EAP-TLS certificates for the key exchange still uses RC4 and greatly ups the security factor, but much like rekeying times, sadly MikroTik does not support it.
So in the world of Mikrotik, IPSec really is the only option for a decently secure VPN tunnel. JTroyBailey hit the nail on the head, IPSec is only a security policy, not a tunnel, that is why it is usually paired with either L2TP or ESP to handle the actual data transmission. If you really want another option, you can look into SSTP, but IMHO, I find the hassle of dealing with the certificates usually outweighs the pain of setting up IPSec.