The only way to get past this just like in stock markets is volume. If there isn't volume it is easily manipulated by these bots.
With volume, bots have a hard time keeping up and adjusting to all of the action which sometimes ends up with the person controlling the bots to actually lose money/value because the bots are not fast enough.
You can sometimes fight the bots by doing small transactions.
I think the problem with alt-coins is that there are just way to many. Like everyone and their grandma has created an alt-coin. It really gives the crypto currency a bad name, and it takes attention away from real game changers, real alt-coins looking to revolutionize currency and transactions. Exchanges/Markets need to stop accepting everything and maybe have some sort of qualifications to get listed. Qualifications like proof of concept and real world application of the coin, etc.
Good Point.
How about a coin that is (more) resilient to manipulation?
For example, put in a delay factor.
The bigger the transaction, the more delay.
A whale's nightmare.