Primitive algo trading got blamed for the crash of 87, and we still have a legacy of obsolete and/or dumb rules from that, coupled with a lack of any idea of what rules would be good for the future.
Puco has a point about crowd momentum being an inherently dangerous thing, but I believe that not only will proprietary AT grow as a % of volume, it will come to dominate trading.
This is because components of AT are applicable even when we are dealing with investment strategies that have days or even month cycles, not just milliseconds.
Several firms now offer the part of AT systems that minimise market impact as a service. Timing a trade to be at the "right" point over a multi day period follows from that.
Ironically, algotrading may actually be partly driven by regulation.
In Europe there is a directive for "best execution" that requires managers to demonstrate that they got the best price for their clients.
Automation makes this easier, and just as importantly, you have an audit trail that supports the case that you obeyed these rules.
In all markets there are rules about market manipulation, and trade automation is on hand to help you avoid being seen as breaching those regulations.
Also there is more regulation on risk, and more invasive risk management to the point where no trader can possibly understand which trades he is "allowed" to do at any point in time, and the periods for exposure limit updates will move towards being near real time, so that one minute you will be allowed to do a trade, the next minute you will not, then back again, or not.
Humans will struggle to cope with that.
So my view is that regulation will act to reduce "seat of the pants" trading by humans because it is harder to prove that it obeyed the rules.
I recall some years ago a semi-serious suggestion that the US tax code be abolished, and replaced with the software that implements it. A law is of course just a program, so why not cut out the error-prone task of converting sloppy English to code ?
The tax law would be whatever the tax system did, we're almost there already, would save quite literally billions, and probably be fairer.
At one point the British Nationality Act was released as an expert system, and now the points based system to get a UK work permit is in effect a computer system with the people merely providing input.
Isaac Asimov would be so happy.