Eomni,
After your training, you will graduate with either a CPL or a MPL, depending on which route you choose. Both licences eventually mature into ATPLs. Be very careful about muddling up a CPL and ATPL - they are not the same thing.
How would either route affect your future career? It all depends on how long you would expect to stay at Flybe, or any other operator, before you planned to move on to the next stage of your career.
After you have achieved approx 1500hrs and met the eligibility criteria to upgrade your licence (whether MPL or CPL), you will have the ATPL exactly the same as every other pilot. Once you have the ATPL, most operators are only interested in your experience and aircraft types, not which route you chose for training. At Flybe, under 'normal' circumstances in a healthy aviation marketplace, gaining your ATPL would take between 2 and 2 1/2 years on average. Regardless of your chosen training route, at this stage you would still be bonded to the airline.
If the MPL interests you, research it carefully. If all you desire is an airline job in a multi-crew environment, then it may be the licence you wish to pursue. If however, you wish to have the opportunity to indulge in single pilot ops (whether commercial or just for fun), then you would have to conduct additional training and testing in order to qualify for the necessary ratings, which are granted automatically with a CPL. Given that you are having to borrow 100% of your funding, I very much doubt you would be able to afford any such indulgences as private GA flying anyway.
As to the respective risks associated with both schemes, at present it is probably 6 and two 3s. The MPL comes with a commitment of training support and as close to a guarantee of employment anyone can get in the current job market, but at the cost of limiting your employment options in the short term to one type. The CPL leaves more doors open to you, but at present, there are no jobs behind the vast majority of those doors, unless you wish to buy a type rating and place your trust in the hands of some very unscrupulous operators.
It is possible to convert the MPL to a CPL at any stage, for a cost, and the training providers should all be offering this as an option.
Last edited by Otto Throttle; 20th Feb 2010 at 10:27.