I'm a financial adviser and there really hasn't been much of a pick up with Junior ISA's. Not many providers have brought in to the concept and so do not offer them, additionally the investment choices you have available tend to be more limited. The trouble with this is that you're effectively locked in to a Junior ISA until their 18. The popularity could drop even further and you could be stuck with archaic investment and charging propositions (see Stakeholder pension)
The fact they are tax free sounds great, but realistically any investment in your childs name would be tax free unless they earnt more than £9,440 pa. The only exception being money from a parent that earns more than £100pa interest (you can get a relative to contribute and this rule does not apply).
The thing that alot of people dislike with the product is that at age 18 it becomes the childs money. If they wanted to take it out and just have a huge bender in Ibiza the money is legally theirs and there is nothing you can do to stop them.
One good idea thats been mentioned is to contribute £3,600 pa into a childs pension. In all likelihood by the time your child retires they will not be able to rely on state pension benefit and will have to contribute a significant portion of their income towards a private pension. Giving them a leg up will have a huge impact on their monthly expenditure for the rest of their lives.
In terms of investment, a good single manager portfolio of funds is the best approach. Not sure how this would work on a DIY basis, I review and rebalance my client's on an ongoing basis but have a team of fund analysts that provide me a shortlist of top quartile funds for each sector. Certain fund supermarkets offer similar recommendations but can be really expensive (Hargreaves Lansdown have a great proposition but have got in some hot water for concealing their fees) A good all in one approach may be a multi-manager fund, the Jupiter Merlin range have performed consistently well.