It is not a question of which is "better". You have not identified the model of Agilent 1260 series system you are comparing it to (and there are many). However, in general, the Waters Alliance 2695 is an academic grade system and most of the Agilent 1260 HPLC modules are considered research grade modules (higher performance). The Alliance systems are a much older design which are harder to service and maintain (esp for novice to intermediate users). Their pumps use conventional check valves, their A/S uses an older low pressure glass syringe based system and they require more training to use effectively.
In making a product choice decision you should consult with a local expert at your company or school who is familiar with your intended applications, uses and level of training. They should be able to review your request in more detail and provide you with constructive advice. Asking for general opinions on general matters usually does not provide good input that is applicable to your specific needs.